Question: new package for generating interactive HTML reports
0
gravatar for Josh Kaminker
6.8 years ago by
Josh Kaminker20 wrote:
Hi all, We present a new R package, ReportingTools<http: www.bioconductor.org="" packages="" devel="" bioc="" html="" re="" portingtools.html="">, for transforming the output of various Bioconductor packages into interactive web pages. We have found this package very useful in our collaborations with both bench and other computational scientists. Examples and instructions for generating output using this package can be found here: http://research-pub.gene.com/ReportingTools/ With just three lines of user code, rich HTML documents can be generated from the result objects produced by several standard Bioconductor packages including edgeR, limma, GOstats, and GSEAlm. By default, ReportingTools reports include hyperlinks to relevant external databases and are highly interactive through the use of filtering and sorting options provided by open source javascript libraries. Supporting javascript and css libraries are included with all reports, allowing them to be examined on a local computer without a network connection. Additionally, in-line graphics have been developed to accompany statistical results to allow convenient visual inspection of underlying raw data. ReportingTools output is highly customizable and this package can be used equally well to share results from automated pipeline processes or individual customized analyses. We are very interested in receiving your feedback including feature requests for this package. Best regards, Josh Kaminker Melanie Huntley Jason Hackney Jessica Larson Christina Chaivorapol -- Josh Kaminker Scientist Department of Bioinformatics and Comp. Biology Genentech Inc. 1 DNA Way South San Francisco, CA 94080 tel.: +1 650 467 8921 fax: +1 650 225 5389 [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.8 years ago by Malcolm Cook1.5k • written 6.8 years ago by Josh Kaminker20
Answer: new package for generating interactive HTML reports
0
gravatar for Steve Lianoglou
6.8 years ago by
Denali
Steve Lianoglou12k wrote:
Cool! On Thu, Jan 10, 2013 at 6:49 PM, Josh Kaminker <kaminker.josh at="" gene.com=""> wrote: > Hi all, > > We present a new R package, > ReportingTools<http: www.bioconductor.org="" packages="" devel="" bioc="" html="" reportingtools.html="">, > for transforming the output of various Bioconductor packages into > interactive web pages. We have found this package very useful in our > collaborations with both bench and other computational scientists. Examples > and instructions for generating output using this package can be found > here: http://research-pub.gene.com/ReportingTools/ > > With just three lines of user code, rich HTML documents can be generated > from the result objects produced by several standard Bioconductor packages > including edgeR, limma, GOstats, and GSEAlm. By default, ReportingTools > reports include hyperlinks to relevant external databases and are highly > interactive through the use of filtering and sorting options provided by > open source javascript libraries. Supporting javascript and css libraries > are included with all reports, allowing them to be examined on a local > computer without a network connection. Additionally, in-line graphics have > been developed to accompany statistical results to allow convenient visual > inspection of underlying raw data. ReportingTools output is highly > customizable and this package can be used equally well to share results > from automated pipeline processes or individual customized analyses. > > We are very interested in receiving your feedback including feature > requests for this package. > > Best regards, > > Josh Kaminker > Melanie Huntley > Jason Hackney > Jessica Larson > Christina Chaivorapol > > > -- > Josh Kaminker > Scientist > Department of Bioinformatics and Comp. Biology > Genentech Inc. > 1 DNA Way > South San Francisco, CA 94080 > tel.: +1 650 467 8921 > fax: +1 650 225 5389 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENTlink written 6.8 years ago by Steve Lianoglou12k
Answer: new package for generating interactive HTML reports
0
gravatar for Xavier de Pedro
6.8 years ago by
Xavier de Pedro50 wrote:
Dear Josh & co.: Thanks for producing such a package, it looks promising indeed! I see that it uses jquery data tables, and the live filtering of the data is very fast (nice!). I have a few quick questions, after a quick review of your vignette and examples: Have you experienced any issues when the data set contained in the browser is very large (regardless that you set the browser to display just 10 records at a time; I understand that the whole data set is loaded in the browser)? And in my relaxed todo list (without hurries) I had the idea to create a similar package to produce wiki syntax for tables from R data frames, and to display png (or svg) images within pages to be displayed through wiki engines (with it's appropriated syntax for the wiki engine of interest). A few years ago I had to do that and I produced some custom function 'ad hoc' without releasing it (yet) in any R package. In our example, we run r scripts through Tiki (wiki) pages, through PluginR, but the output is either bare text (so far) or images (png or svg), and any modification is handled by R commands by hand. And a function to produce the "Fancy Tables" that Tiki can produce with "JQuery Sortable Tables" is needed ( http://doc.tiki.org/PluginFancyTable ). I foresee that maybe the datatable jquery plugin could be even better for that, since it contains pagination and live filtering, which can be very very handy!. And maybe you are open to receive improvements/extensions to your package to support other ways to produce the tables required for better integration for wiki engines such as Tiki? Or should I fork from your package? Thanks in advanced, and congratulations for the generic package that you created. Xavier On 11/01/13 00:49, Josh Kaminker wrote: > Hi all, > > We present a new R package, > ReportingTools<http: www.bioconductor.org="" packages="" devel="" bioc="" html="" reportingtools.html="">, > for transforming the output of various Bioconductor packages into > interactive web pages. We have found this package very useful in our > collaborations with both bench and other computational scientists. Examples > and instructions for generating output using this package can be found > here: http://research-pub.gene.com/ReportingTools/ > > With just three lines of user code, rich HTML documents can be generated > from the result objects produced by several standard Bioconductor packages > including edgeR, limma, GOstats, and GSEAlm. By default, ReportingTools > reports include hyperlinks to relevant external databases and are highly > interactive through the use of filtering and sorting options provided by > open source javascript libraries. Supporting javascript and css libraries > are included with all reports, allowing them to be examined on a local > computer without a network connection. Additionally, in-line graphics have > been developed to accompany statistical results to allow convenient visual > inspection of underlying raw data. ReportingTools output is highly > customizable and this package can be used equally well to share results > from automated pipeline processes or individual customized analyses. > > We are very interested in receiving your feedback including feature > requests for this package. > > Best regards, > > Josh Kaminker > Melanie Huntley > Jason Hackney > Jessica Larson > Christina Chaivorapol > > -- Xavier de Pedro Puente, Ph.D. Statistics and Bioinformatics Unit (UEB) High Technology Unit (UAT) Vall d'Hebron Research Institute (VHIR). Mediterranean Building Passeig de la Vall d'Hebron, 119-129 08035 Barcelona. Catalonia. Spain Ph. +34 934894007 / Fax +34 934894015 xavier.depedro at vhir.org http://ueb.vhir.org
ADD COMMENTlink written 6.8 years ago by Xavier de Pedro50
The package is extensible to the point that you could simply create a new type of report that is output as some wiki language, so it wouldn't be necessary to fork or modify ReportingTools. If there are internal utilities for generating data tables that might be usefully shared, they could be exposed, or at least factored out for ":::" access. Michael On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro <xavier.depedro@vhir.org>wrote: > Dear Josh & co.: > > Thanks for producing such a package, it looks promising indeed! > > I see that it uses jquery data tables, and the live filtering of the data > is very fast (nice!). > I have a few quick questions, after a quick review of your vignette and > examples: > > Have you experienced any issues when the data set contained in the browser > is very large (regardless that you set the browser to display just 10 > records at a time; I understand that the whole data set is loaded in the > browser)? > > And in my relaxed todo list (without hurries) I had the idea to create a > similar package to produce wiki syntax for tables from R data frames, and > to display png (or svg) images within pages to be displayed through wiki > engines (with it's appropriated syntax for the wiki engine of interest). A > few years ago I had to do that and I produced some custom function 'ad hoc' > without releasing it (yet) in any R package. In our example, we run r > scripts through Tiki (wiki) pages, through PluginR, but the output is > either bare text (so far) or images (png or svg), and any modification is > handled by R commands by hand. And a function to produce the "Fancy Tables" > that Tiki can produce with "JQuery Sortable Tables" is needed ( > http://doc.tiki.org/**PluginFancyTable<http: doc.tiki.org="" pluginfan="" cytable="">). I foresee that maybe the datatable jquery plugin could be even better > for that, since it contains pagination and live filtering, which can be > very very handy!. > > And maybe you are open to receive improvements/extensions to your package > to support other ways to produce the tables required for better integration > for wiki engines such as Tiki? Or should I fork from your package? > > Thanks in advanced, and congratulations for the generic package that you > created. > > Xavier > > > On 11/01/13 00:49, Josh Kaminker wrote: > >> Hi all, >> >> We present a new R package, >> ReportingTools<http: www.**bioconductor.org="" packages="" **devel="" bioc="" html="" *="">> *ReportingTools.html<http: www.bioconductor.org="" packages="" devel="" bio="" c="" html="" reportingtools.html=""> >> >, >> for transforming the output of various Bioconductor packages into >> interactive web pages. We have found this package very useful in our >> collaborations with both bench and other computational scientists. >> Examples >> and instructions for generating output using this package can be found >> here: http://research-pub.gene.com/**ReportingTools/<http :="" research-pub.gene.com="" reportingtools=""/> >> >> With just three lines of user code, rich HTML documents can be generated >> from the result objects produced by several standard Bioconductor packages >> including edgeR, limma, GOstats, and GSEAlm. By default, ReportingTools >> reports include hyperlinks to relevant external databases and are highly >> interactive through the use of filtering and sorting options provided by >> open source javascript libraries. Supporting javascript and css libraries >> are included with all reports, allowing them to be examined on a local >> computer without a network connection. Additionally, in-line graphics >> have >> been developed to accompany statistical results to allow convenient visual >> inspection of underlying raw data. ReportingTools output is highly >> customizable and this package can be used equally well to share results >> from automated pipeline processes or individual customized analyses. >> >> We are very interested in receiving your feedback including feature >> requests for this package. >> >> Best regards, >> >> Josh Kaminker >> Melanie Huntley >> Jason Hackney >> Jessica Larson >> Christina Chaivorapol >> >> >> > > -- > Xavier de Pedro Puente, Ph.D. > Statistics and Bioinformatics Unit (UEB) > High Technology Unit (UAT) > Vall d'Hebron Research Institute (VHIR). Mediterranean Building > Passeig de la Vall d'Hebron, 119-129 > 08035 Barcelona. Catalonia. Spain > Ph. +34 934894007 / Fax +34 934894015 > xavier.depedro@vhir.org > http://ueb.vhir.org > > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
ADD REPLYlink written 6.8 years ago by Michael Lawrence11k
Hi Xavier, Thanks for your comments and suggestions! In response to your question about issues when the data in the browser is very large - yes, we have observed sluggish behavior when, for example, you have a table with 20,000+ rows and many columns, including graphics. And in fact, the Chrome browser seems to give us the most trouble in those cases. We'd love to hear about ways to improve this behavior, if anyone has ideas. Melanie On Fri, Jan 11, 2013 at 7:19 AM, Michael Lawrence <lawrence.michael@gene.com> wrote: > The package is extensible to the point that you could simply create a new > type of report that is output as some wiki language, so it wouldn't be > necessary to fork or modify ReportingTools. If there are internal utilities > for generating data tables that might be usefully shared, they could be > exposed, or at least factored out for ":::" access. > > Michael > > > On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro <xavier.depedro@vhir.org> >wrote: > > > Dear Josh & co.: > > > > Thanks for producing such a package, it looks promising indeed! > > > > I see that it uses jquery data tables, and the live filtering of the data > > is very fast (nice!). > > I have a few quick questions, after a quick review of your vignette and > > examples: > > > > Have you experienced any issues when the data set contained in the > browser > > is very large (regardless that you set the browser to display just 10 > > records at a time; I understand that the whole data set is loaded in the > > browser)? > > > > And in my relaxed todo list (without hurries) I had the idea to create a > > similar package to produce wiki syntax for tables from R data frames, and > > to display png (or svg) images within pages to be displayed through wiki > > engines (with it's appropriated syntax for the wiki engine of interest). > A > > few years ago I had to do that and I produced some custom function 'ad > hoc' > > without releasing it (yet) in any R package. In our example, we run r > > scripts through Tiki (wiki) pages, through PluginR, but the output is > > either bare text (so far) or images (png or svg), and any modification is > > handled by R commands by hand. And a function to produce the "Fancy > Tables" > > that Tiki can produce with "JQuery Sortable Tables" is needed ( > > http://doc.tiki.org/**PluginFancyTable< > http://doc.tiki.org/PluginFancyTable>). I foresee that maybe the > datatable jquery plugin could be even better > > for that, since it contains pagination and live filtering, which can be > > very very handy!. > > > > And maybe you are open to receive improvements/extensions to your package > > to support other ways to produce the tables required for better > integration > > for wiki engines such as Tiki? Or should I fork from your package? > > > > Thanks in advanced, and congratulations for the generic package that you > > created. > > > > Xavier > > > > > > On 11/01/13 00:49, Josh Kaminker wrote: > > > >> Hi all, > >> > >> We present a new R package, > >> ReportingTools<http: www.**=""> bioconductor.org/packages/**devel/bioc/html/* > >> *ReportingTools.html< > http://www.bioconductor.org/packages/devel/bioc/html/ReportingTools. html> > >> >, > >> for transforming the output of various Bioconductor packages into > >> interactive web pages. We have found this package very useful in our > >> collaborations with both bench and other computational scientists. > >> Examples > >> and instructions for generating output using this package can be found > >> here: http://research-pub.gene.com/**ReportingTools/< > http://research-pub.gene.com/ReportingTools/> > >> > >> With just three lines of user code, rich HTML documents can be generated > >> from the result objects produced by several standard Bioconductor > packages > >> including edgeR, limma, GOstats, and GSEAlm. By default, ReportingTools > >> reports include hyperlinks to relevant external databases and are highly > >> interactive through the use of filtering and sorting options provided by > >> open source javascript libraries. Supporting javascript and css > libraries > >> are included with all reports, allowing them to be examined on a local > >> computer without a network connection. Additionally, in-line graphics > >> have > >> been developed to accompany statistical results to allow convenient > visual > >> inspection of underlying raw data. ReportingTools output is highly > >> customizable and this package can be used equally well to share results > >> from automated pipeline processes or individual customized analyses. > >> > >> We are very interested in receiving your feedback including feature > >> requests for this package. > >> > >> Best regards, > >> > >> Josh Kaminker > >> Melanie Huntley > >> Jason Hackney > >> Jessica Larson > >> Christina Chaivorapol > >> > >> > >> > > > > -- > > Xavier de Pedro Puente, Ph.D. > > Statistics and Bioinformatics Unit (UEB) > > High Technology Unit (UAT) > > Vall d'Hebron Research Institute (VHIR). Mediterranean Building > > Passeig de la Vall d'Hebron, 119-129 > > 08035 Barcelona. Catalonia. Spain > > Ph. +34 934894007 / Fax +34 934894015 > > xavier.depedro@vhir.org > > http://ueb.vhir.org > > > > > > ______________________________**_________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/**listinfo/bioconductor< > https://stat.ethz.ch/mailman/listinfo/bioconductor> > > Search the archives: http://news.gmane.org/gmane.** > > science.biology.informatics.**conductor< > http://news.gmane.org/gmane.science.biology.informatics.conductor> > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Melanie Huntley, Ph.D Bioinformatics and Computational Biology Genentech, Inc. huntley.melanie@gene.com [[alternative HTML version deleted]]
ADD REPLYlink written 6.8 years ago by Melanie Huntley30
On Fri, Jan 11, 2013 at 11:07 AM, Melanie Huntley <huntley.melanie at="" gene.com=""> wrote: > Hi Xavier, > > Thanks for your comments and suggestions! > > In response to your question about issues when the data in the browser is > very large - yes, we have observed sluggish behavior when, for example, you > have a table with 20,000+ rows and many columns, including graphics. And in > fact, the Chrome browser seems to give us the most trouble in those cases. > > We'd love to hear about ways to improve this behavior, if anyone has ideas. Hi, Melanie. The "extra" scroller for datatables allows scrolling of VERY large datasets because only a small portion of the entire dataset is sent to the client at one time. The server simply responds to requests for data as the dataset scrolls on the client. The details are here: http://datatables.net/release-datatables/extras/Scroller/server- side_processing.html This would require a server that responds to queries be running while the client is interacting with the data. Sean > On Fri, Jan 11, 2013 at 7:19 AM, Michael Lawrence <lawrence.michael at="" gene.com="">> wrote: > >> The package is extensible to the point that you could simply create a new >> type of report that is output as some wiki language, so it wouldn't be >> necessary to fork or modify ReportingTools. If there are internal utilities >> for generating data tables that might be usefully shared, they could be >> exposed, or at least factored out for ":::" access. >> >> Michael >> >> >> On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro <xavier.depedro at="" vhir.org="">> >wrote: >> >> > Dear Josh & co.: >> > >> > Thanks for producing such a package, it looks promising indeed! >> > >> > I see that it uses jquery data tables, and the live filtering of the data >> > is very fast (nice!). >> > I have a few quick questions, after a quick review of your vignette and >> > examples: >> > >> > Have you experienced any issues when the data set contained in the >> browser >> > is very large (regardless that you set the browser to display just 10 >> > records at a time; I understand that the whole data set is loaded in the >> > browser)? >> > >> > And in my relaxed todo list (without hurries) I had the idea to create a >> > similar package to produce wiki syntax for tables from R data frames, and >> > to display png (or svg) images within pages to be displayed through wiki >> > engines (with it's appropriated syntax for the wiki engine of interest). >> A >> > few years ago I had to do that and I produced some custom function 'ad >> hoc' >> > without releasing it (yet) in any R package. In our example, we run r >> > scripts through Tiki (wiki) pages, through PluginR, but the output is >> > either bare text (so far) or images (png or svg), and any modification is >> > handled by R commands by hand. And a function to produce the "Fancy >> Tables" >> > that Tiki can produce with "JQuery Sortable Tables" is needed ( >> > http://doc.tiki.org/**PluginFancyTable< >> http://doc.tiki.org/PluginFancyTable>). I foresee that maybe the >> datatable jquery plugin could be even better >> > for that, since it contains pagination and live filtering, which can be >> > very very handy!. >> > >> > And maybe you are open to receive improvements/extensions to your package >> > to support other ways to produce the tables required for better >> integration >> > for wiki engines such as Tiki? Or should I fork from your package? >> > >> > Thanks in advanced, and congratulations for the generic package that you >> > created. >> > >> > Xavier >> > >> > >> > On 11/01/13 00:49, Josh Kaminker wrote: >> > >> >> Hi all, >> >> >> >> We present a new R package, >> >> ReportingTools<http: www.**="">> bioconductor.org/packages/**devel/bioc/html/* >> >> *ReportingTools.html< >> http://www.bioconductor.org/packages/devel/bioc/html/ReportingTools .html> >> >> >, >> >> for transforming the output of various Bioconductor packages into >> >> interactive web pages. We have found this package very useful in our >> >> collaborations with both bench and other computational scientists. >> >> Examples >> >> and instructions for generating output using this package can be found >> >> here: http://research-pub.gene.com/**ReportingTools/< >> http://research-pub.gene.com/ReportingTools/> >> >> >> >> With just three lines of user code, rich HTML documents can be generated >> >> from the result objects produced by several standard Bioconductor >> packages >> >> including edgeR, limma, GOstats, and GSEAlm. By default, ReportingTools >> >> reports include hyperlinks to relevant external databases and are highly >> >> interactive through the use of filtering and sorting options provided by >> >> open source javascript libraries. Supporting javascript and css >> libraries >> >> are included with all reports, allowing them to be examined on a local >> >> computer without a network connection. Additionally, in-line graphics >> >> have >> >> been developed to accompany statistical results to allow convenient >> visual >> >> inspection of underlying raw data. ReportingTools output is highly >> >> customizable and this package can be used equally well to share results >> >> from automated pipeline processes or individual customized analyses. >> >> >> >> We are very interested in receiving your feedback including feature >> >> requests for this package. >> >> >> >> Best regards, >> >> >> >> Josh Kaminker >> >> Melanie Huntley >> >> Jason Hackney >> >> Jessica Larson >> >> Christina Chaivorapol >> >> >> >> >> >> >> > >> > -- >> > Xavier de Pedro Puente, Ph.D. >> > Statistics and Bioinformatics Unit (UEB) >> > High Technology Unit (UAT) >> > Vall d'Hebron Research Institute (VHIR). Mediterranean Building >> > Passeig de la Vall d'Hebron, 119-129 >> > 08035 Barcelona. Catalonia. Spain >> > Ph. +34 934894007 / Fax +34 934894015 >> > xavier.depedro at vhir.org >> > http://ueb.vhir.org >> > >> > >> > ______________________________**_________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/**listinfo/bioconductor< >> https://stat.ethz.ch/mailman/listinfo/bioconductor> >> > Search the archives: http://news.gmane.org/gmane.** >> > science.biology.informatics.**conductor< >> http://news.gmane.org/gmane.science.biology.informatics.conductor> >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > Melanie Huntley, Ph.D > Bioinformatics and Computational Biology > Genentech, Inc. > huntley.melanie at gene.com > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.8 years ago by Sean Davis21k
Hi Sean, There certainly seem to be more available options to speed things up if we require the hard work to be done server side - we were considering this in the initial phases of the package devel. Our thinking was to keep things as user friendly as possible to start (ie. keep things client side) - but the trade-off has been a decrease in responsiveness for very large datasets. Perhaps we should revisit the server option again for the next release if we don't find a client side solution. Thanks, Melanie On Fri, Jan 11, 2013 at 10:23 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > Hi, Melanie. > > The "extra" scroller for datatables allows scrolling of VERY large > datasets because only a small portion of the entire dataset is sent to > the client at one time. The server simply responds to requests for > data as the dataset scrolls on the client. The details are here: > > > http://datatables.net/release-datatables/extras/Scroller/server- side_processing.html > > This would require a server that responds to queries be running while > the client is interacting with the data. > > Sean > > > > > On Fri, Jan 11, 2013 at 7:19 AM, Michael Lawrence < > lawrence.michael@gene.com > >> wrote: > > > >> The package is extensible to the point that you could simply create a > new > >> type of report that is output as some wiki language, so it wouldn't be > >> necessary to fork or modify ReportingTools. If there are internal > utilities > >> for generating data tables that might be usefully shared, they could be > >> exposed, or at least factored out for ":::" access. > >> > >> Michael > >> > >> > >> On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro < > xavier.depedro@vhir.org > >> >wrote: > >> > >> > Dear Josh & co.: > >> > > >> > Thanks for producing such a package, it looks promising indeed! > >> > > >> > I see that it uses jquery data tables, and the live filtering of the > data > >> > is very fast (nice!). > >> > I have a few quick questions, after a quick review of your vignette > and > >> > examples: > >> > > >> > Have you experienced any issues when the data set contained in the > >> browser > >> > is very large (regardless that you set the browser to display just 10 > >> > records at a time; I understand that the whole data set is loaded in > the > >> > browser)? > >> > > >> > And in my relaxed todo list (without hurries) I had the idea to > create a > >> > similar package to produce wiki syntax for tables from R data frames, > and > >> > to display png (or svg) images within pages to be displayed through > wiki > >> > engines (with it's appropriated syntax for the wiki engine of > interest). > >> A > >> > few years ago I had to do that and I produced some custom function 'ad > >> hoc' > >> > without releasing it (yet) in any R package. In our example, we run r > >> > scripts through Tiki (wiki) pages, through PluginR, but the output is > >> > either bare text (so far) or images (png or svg), and any > modification is > >> > handled by R commands by hand. And a function to produce the "Fancy > >> Tables" > >> > that Tiki can produce with "JQuery Sortable Tables" is needed ( > >> > http://doc.tiki.org/**PluginFancyTable< > >> http://doc.tiki.org/PluginFancyTable>). I foresee that maybe the > >> datatable jquery plugin could be even better > >> > for that, since it contains pagination and live filtering, which can > be > >> > very very handy!. > >> > > >> > And maybe you are open to receive improvements/extensions to your > package > >> > to support other ways to produce the tables required for better > >> integration > >> > for wiki engines such as Tiki? Or should I fork from your package? > >> > > >> > Thanks in advanced, and congratulations for the generic package that > you > >> > created. > >> > > >> > Xavier > >> > > >> > > >> > On 11/01/13 00:49, Josh Kaminker wrote: > >> > > >> >> Hi all, > >> >> > >> >> We present a new R package, > >> >> ReportingTools<http: www.**=""> >> bioconductor.org/packages/**devel/bioc/html/* > >> >> *ReportingTools.html< > >> > http://www.bioconductor.org/packages/devel/bioc/html/ReportingTools. html> > >> >> >, > >> >> for transforming the output of various Bioconductor packages into > >> >> interactive web pages. We have found this package very useful in our > >> >> collaborations with both bench and other computational scientists. > >> >> Examples > >> >> and instructions for generating output using this package can be > found > >> >> here: http://research-pub.gene.com/**ReportingTools/< > >> http://research-pub.gene.com/ReportingTools/> > >> >> > >> >> With just three lines of user code, rich HTML documents can be > generated > >> >> from the result objects produced by several standard Bioconductor > >> packages > >> >> including edgeR, limma, GOstats, and GSEAlm. By default, > ReportingTools > >> >> reports include hyperlinks to relevant external databases and are > highly > >> >> interactive through the use of filtering and sorting options > provided by > >> >> open source javascript libraries. Supporting javascript and css > >> libraries > >> >> are included with all reports, allowing them to be examined on a > local > >> >> computer without a network connection. Additionally, in-line > graphics > >> >> have > >> >> been developed to accompany statistical results to allow convenient > >> visual > >> >> inspection of underlying raw data. ReportingTools output is highly > >> >> customizable and this package can be used equally well to share > results > >> >> from automated pipeline processes or individual customized analyses. > >> >> > >> >> We are very interested in receiving your feedback including feature > >> >> requests for this package. > >> >> > >> >> Best regards, > >> >> > >> >> Josh Kaminker > >> >> Melanie Huntley > >> >> Jason Hackney > >> >> Jessica Larson > >> >> Christina Chaivorapol > >> >> > >> >> > >> >> > >> > > >> > -- > >> > Xavier de Pedro Puente, Ph.D. > >> > Statistics and Bioinformatics Unit (UEB) > >> > High Technology Unit (UAT) > >> > Vall d'Hebron Research Institute (VHIR). Mediterranean Building > >> > Passeig de la Vall d'Hebron, 119-129 > >> > 08035 Barcelona. Catalonia. Spain > >> > Ph. +34 934894007 / Fax +34 934894015 > >> > xavier.depedro@vhir.org > >> > http://ueb.vhir.org > >> > > >> > > >> > ______________________________**_________________ > >> > Bioconductor mailing list > >> > Bioconductor@r-project.org > >> > https://stat.ethz.ch/mailman/**listinfo/bioconductor< > >> https://stat.ethz.ch/mailman/listinfo/bioconductor> > >> > Search the archives: http://news.gmane.org/gmane.** > >> > science.biology.informatics.**conductor< > >> http://news.gmane.org/gmane.science.biology.informatics.conductor> > >> > > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > > > -- > > Melanie Huntley, Ph.D > > Bioinformatics and Computational Biology > > Genentech, Inc. > > huntley.melanie@gene.com > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Melanie Huntley, Ph.D Bioinformatics and Computational Biology Genentech, Inc. huntley.melanie@gene.com [[alternative HTML version deleted]]
ADD REPLYlink written 6.8 years ago by Melanie Huntley30
On 01/11/2013 10:37 AM, Melanie Huntley wrote: > Hi Sean, > > There certainly seem to be more available options to speed things up if we > require the hard work to be done server side - we were considering this in > the initial phases of the package devel. > > Our thinking was to keep things as user friendly as possible to start (ie. > keep things client side) - but the trade-off has been a decrease in > responsiveness for very large datasets. Perhaps we should revisit the > server option again for the next release if we don't find a client side > solution. really just shooting from the hip here, but the R package 'shiny' seems to be a very nice way to deploy R client / server apps; under the hood I think it's using the R 'websockets' library as a modern way to communicate. Martin > > Thanks, > Melanie > > On Fri, Jan 11, 2013 at 10:23 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> >> Hi, Melanie. >> >> The "extra" scroller for datatables allows scrolling of VERY large >> datasets because only a small portion of the entire dataset is sent to >> the client at one time. The server simply responds to requests for >> data as the dataset scrolls on the client. The details are here: >> >> >> http://datatables.net/release-datatables/extras/Scroller/server- side_processing.html >> >> This would require a server that responds to queries be running while >> the client is interacting with the data. >> >> Sean >> >> >> >>> On Fri, Jan 11, 2013 at 7:19 AM, Michael Lawrence < >> lawrence.michael at gene.com >>>> wrote: >>> >>>> The package is extensible to the point that you could simply create a >> new >>>> type of report that is output as some wiki language, so it wouldn't be >>>> necessary to fork or modify ReportingTools. If there are internal >> utilities >>>> for generating data tables that might be usefully shared, they could be >>>> exposed, or at least factored out for ":::" access. >>>> >>>> Michael >>>> >>>> >>>> On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro < >> xavier.depedro at vhir.org >>>>> wrote: >>>> >>>>> Dear Josh & co.: >>>>> >>>>> Thanks for producing such a package, it looks promising indeed! >>>>> >>>>> I see that it uses jquery data tables, and the live filtering of the >> data >>>>> is very fast (nice!). >>>>> I have a few quick questions, after a quick review of your vignette >> and >>>>> examples: >>>>> >>>>> Have you experienced any issues when the data set contained in the >>>> browser >>>>> is very large (regardless that you set the browser to display just 10 >>>>> records at a time; I understand that the whole data set is loaded in >> the >>>>> browser)? >>>>> >>>>> And in my relaxed todo list (without hurries) I had the idea to >> create a >>>>> similar package to produce wiki syntax for tables from R data frames, >> and >>>>> to display png (or svg) images within pages to be displayed through >> wiki >>>>> engines (with it's appropriated syntax for the wiki engine of >> interest). >>>> A >>>>> few years ago I had to do that and I produced some custom function 'ad >>>> hoc' >>>>> without releasing it (yet) in any R package. In our example, we run r >>>>> scripts through Tiki (wiki) pages, through PluginR, but the output is >>>>> either bare text (so far) or images (png or svg), and any >> modification is >>>>> handled by R commands by hand. And a function to produce the "Fancy >>>> Tables" >>>>> that Tiki can produce with "JQuery Sortable Tables" is needed ( >>>>> http://doc.tiki.org/**PluginFancyTable< >>>> http://doc.tiki.org/PluginFancyTable>). I foresee that maybe the >>>> datatable jquery plugin could be even better >>>>> for that, since it contains pagination and live filtering, which can >> be >>>>> very very handy!. >>>>> >>>>> And maybe you are open to receive improvements/extensions to your >> package >>>>> to support other ways to produce the tables required for better >>>> integration >>>>> for wiki engines such as Tiki? Or should I fork from your package? >>>>> >>>>> Thanks in advanced, and congratulations for the generic package that >> you >>>>> created. >>>>> >>>>> Xavier >>>>> >>>>> >>>>> On 11/01/13 00:49, Josh Kaminker wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> We present a new R package, >>>>>> ReportingTools<http: www.**="">>>> bioconductor.org/packages/**devel/bioc/html/* >>>>>> *ReportingTools.html< >>>> >> http://www.bioconductor.org/packages/devel/bioc/html/ReportingTools .html> >>>>>>> , >>>>>> for transforming the output of various Bioconductor packages into >>>>>> interactive web pages. We have found this package very useful in our >>>>>> collaborations with both bench and other computational scientists. >>>>>> Examples >>>>>> and instructions for generating output using this package can be >> found >>>>>> here: http://research-pub.gene.com/**ReportingTools/< >>>> http://research-pub.gene.com/ReportingTools/> >>>>>> >>>>>> With just three lines of user code, rich HTML documents can be >> generated >>>>>> from the result objects produced by several standard Bioconductor >>>> packages >>>>>> including edgeR, limma, GOstats, and GSEAlm. By default, >> ReportingTools >>>>>> reports include hyperlinks to relevant external databases and are >> highly >>>>>> interactive through the use of filtering and sorting options >> provided by >>>>>> open source javascript libraries. Supporting javascript and css >>>> libraries >>>>>> are included with all reports, allowing them to be examined on a >> local >>>>>> computer without a network connection. Additionally, in-line >> graphics >>>>>> have >>>>>> been developed to accompany statistical results to allow convenient >>>> visual >>>>>> inspection of underlying raw data. ReportingTools output is highly >>>>>> customizable and this package can be used equally well to share >> results >>>>>> from automated pipeline processes or individual customized analyses. >>>>>> >>>>>> We are very interested in receiving your feedback including feature >>>>>> requests for this package. >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Josh Kaminker >>>>>> Melanie Huntley >>>>>> Jason Hackney >>>>>> Jessica Larson >>>>>> Christina Chaivorapol >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Xavier de Pedro Puente, Ph.D. >>>>> Statistics and Bioinformatics Unit (UEB) >>>>> High Technology Unit (UAT) >>>>> Vall d'Hebron Research Institute (VHIR). Mediterranean Building >>>>> Passeig de la Vall d'Hebron, 119-129 >>>>> 08035 Barcelona. Catalonia. Spain >>>>> Ph. +34 934894007 / Fax +34 934894015 >>>>> xavier.depedro at vhir.org >>>>> http://ueb.vhir.org >>>>> >>>>> >>>>> ______________________________**_________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor> >>>>> Search the archives: http://news.gmane.org/gmane.** >>>>> science.biology.informatics.**conductor< >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor> >>>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >>> >>> -- >>> Melanie Huntley, Ph.D >>> Bioinformatics and Computational Biology >>> Genentech, Inc. >>> huntley.melanie at gene.com >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 6.8 years ago by Martin Morgan ♦♦ 23k
Melanie, I too have employed the jsQuery dataTable. I use emacs org mode to generate reports with embedded tables, all of which are made indiscriminately made scrollable/pageable/searchable with the inclusion of a few style directives in the org file. With the same upsides&downsides you are discussing here. I recommend it for simple standalone html non-interactive reporting. In my experience, tens of thousands of rows are easily handled on chrome browser on local area network. ~Malcolm .-----Original Message----- .From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r-project.org] On Behalf Of Melanie Huntley .Sent: Friday, January 11, 2013 12:37 PM .To: Sean Davis .Cc: Josh Kaminker; Michael Lawrence; Melanie Huntley; bioconductor at r-project.org .Subject: Re: [BioC] new package for generating interactive HTML reports . .Hi Sean, . .There certainly seem to be more available options to speed things up if we .require the hard work to be done server side - we were considering this in .the initial phases of the package devel. . .Our thinking was to keep things as user friendly as possible to start (ie. .keep things client side) - but the trade-off has been a decrease in .responsiveness for very large datasets. Perhaps we should revisit the .server option again for the next release if we don't find a client side .solution. . .Thanks, .Melanie . .On Fri, Jan 11, 2013 at 10:23 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: . .> .> Hi, Melanie. .> .> The "extra" scroller for datatables allows scrolling of VERY large .> datasets because only a small portion of the entire dataset is sent to .> the client at one time. The server simply responds to requests for .> data as the dataset scrolls on the client. The details are here: .> .> .> http://datatables.net/release-datatables/extras/Scroller/server- side_processing.html .> .> This would require a server that responds to queries be running while .> the client is interacting with the data. .> .> Sean .> .> .> .> > On Fri, Jan 11, 2013 at 7:19 AM, Michael Lawrence < .> lawrence.michael at gene.com .> >> wrote: .> > .> >> The package is extensible to the point that you could simply create a .> new .> >> type of report that is output as some wiki language, so it wouldn't be .> >> necessary to fork or modify ReportingTools. If there are internal .> utilities .> >> for generating data tables that might be usefully shared, they could be .> >> exposed, or at least factored out for ":::" access. .> >> .> >> Michael .> >> .> >> .> >> On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro < .> xavier.depedro at vhir.org .> >> >wrote: .> >> .> >> > Dear Josh & co.: .> >> > .> >> > Thanks for producing such a package, it looks promising indeed! .> >> > .> >> > I see that it uses jquery data tables, and the live filtering of the .> data .> >> > is very fast (nice!). .> >> > I have a few quick questions, after a quick review of your vignette .> and .> >> > examples: .> >> > .> >> > Have you experienced any issues when the data set contained in the .> >> browser .> >> > is very large (regardless that you set the browser to display just 10 .> >> > records at a time; I understand that the whole data set is loaded in .> the .> >> > browser)? .> >> > .> >> > And in my relaxed todo list (without hurries) I had the idea to .> create a .> >> > similar package to produce wiki syntax for tables from R data frames, .> and .> >> > to display png (or svg) images within pages to be displayed through .> wiki .> >> > engines (with it's appropriated syntax for the wiki engine of .> interest). .> >> A .> >> > few years ago I had to do that and I produced some custom function 'ad .> >> hoc' .> >> > without releasing it (yet) in any R package. In our example, we run r .> >> > scripts through Tiki (wiki) pages, through PluginR, but the output is .> >> > either bare text (so far) or images (png or svg), and any .> modification is .> >> > handled by R commands by hand. And a function to produce the "Fancy .> >> Tables" .> >> > that Tiki can produce with "JQuery Sortable Tables" is needed ( .> >> > http://doc.tiki.org/**PluginFancyTable< .> >> http://doc.tiki.org/PluginFancyTable>). I foresee that maybe the .> >> datatable jquery plugin could be even better .> >> > for that, since it contains pagination and live filtering, which can .> be .> >> > very very handy!. .> >> > .> >> > And maybe you are open to receive improvements/extensions to your .> package .> >> > to support other ways to produce the tables required for better .> >> integration .> >> > for wiki engines such as Tiki? Or should I fork from your package? .> >> > .> >> > Thanks in advanced, and congratulations for the generic package that .> you .> >> > created. .> >> > .> >> > Xavier .> >> > .> >> > .> >> > On 11/01/13 00:49, Josh Kaminker wrote: .> >> > .> >> >> Hi all, .> >> >> .> >> >> We present a new R package, .> >> >> ReportingTools<http: www.**="" .=""> >> bioconductor.org/packages/**devel/bioc/html/* .> >> >> *ReportingTools.html< .> >> .> http://www.bioconductor.org/packages/devel/bioc/html/ReportingTool s.html> .> >> >> >, .> >> >> for transforming the output of various Bioconductor packages into .> >> >> interactive web pages. We have found this package very useful in our .> >> >> collaborations with both bench and other computational scientists. .> >> >> Examples .> >> >> and instructions for generating output using this package can be .> found .> >> >> here: http://research-pub.gene.com/**ReportingTools/< .> >> http://research-pub.gene.com/ReportingTools/> .> >> >> .> >> >> With just three lines of user code, rich HTML documents can be .> generated .> >> >> from the result objects produced by several standard Bioconductor .> >> packages .> >> >> including edgeR, limma, GOstats, and GSEAlm. By default, .> ReportingTools .> >> >> reports include hyperlinks to relevant external databases and are .> highly .> >> >> interactive through the use of filtering and sorting options .> provided by .> >> >> open source javascript libraries. Supporting javascript and css .> >> libraries .> >> >> are included with all reports, allowing them to be examined on a .> local .> >> >> computer without a network connection. Additionally, in- line .> graphics .> >> >> have .> >> >> been developed to accompany statistical results to allow convenient .> >> visual .> >> >> inspection of underlying raw data. ReportingTools output is highly .> >> >> customizable and this package can be used equally well to share .> results .> >> >> from automated pipeline processes or individual customized analyses. .> >> >> .> >> >> We are very interested in receiving your feedback including feature .> >> >> requests for this package. .> >> >> .> >> >> Best regards, .> >> >> .> >> >> Josh Kaminker .> >> >> Melanie Huntley .> >> >> Jason Hackney .> >> >> Jessica Larson .> >> >> Christina Chaivorapol .> >> >> .> >> >> .> >> >> .> >> > .> >> > -- .> >> > Xavier de Pedro Puente, Ph.D. .> >> > Statistics and Bioinformatics Unit (UEB) .> >> > High Technology Unit (UAT) .> >> > Vall d'Hebron Research Institute (VHIR). Mediterranean Building .> >> > Passeig de la Vall d'Hebron, 119-129 .> >> > 08035 Barcelona. Catalonia. Spain .> >> > Ph. +34 934894007 / Fax +34 934894015 .> >> > xavier.depedro at vhir.org .> >> > http://ueb.vhir.org .> >> > .> >> > .> >> > ______________________________**_________________ .> >> > Bioconductor mailing list .> >> > Bioconductor at r-project.org .> >> > https://stat.ethz.ch/mailman/**listinfo/bioconductor< .> >> https://stat.ethz.ch/mailman/listinfo/bioconductor> .> >> > Search the archives: http://news.gmane.org/gmane.** .> >> > science.biology.informatics.**conductor< .> >> http://news.gmane.org/gmane.science.biology.informatics.conductor> .> >> > .> >> .> >> [[alternative HTML version deleted]] .> >> .> >> _______________________________________________ .> >> Bioconductor mailing list .> >> Bioconductor at r-project.org .> >> https://stat.ethz.ch/mailman/listinfo/bioconductor .> >> Search the archives: .> >> http://news.gmane.org/gmane.science.biology.informatics.conductor .> >> .> > .> > .> > .> > -- .> > Melanie Huntley, Ph.D .> > Bioinformatics and Computational Biology .> > Genentech, Inc. .> > huntley.melanie at gene.com .> > .> > [[alternative HTML version deleted]] .> > .> > _______________________________________________ .> > Bioconductor mailing list .> > Bioconductor at r-project.org .> > https://stat.ethz.ch/mailman/listinfo/bioconductor .> > Search the archives: .> http://news.gmane.org/gmane.science.biology.informatics.conductor .> . . . .-- .Melanie Huntley, Ph.D .Bioinformatics and Computational Biology .Genentech, Inc. .huntley.melanie at gene.com . . [[alternative HTML version deleted]] . ._______________________________________________ .Bioconductor mailing list .Bioconductor at r-project.org .https://stat.ethz.ch/mailman/listinfo/bioconductor .Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.8 years ago by Malcolm Cook1.5k
On Fri, Jan 11, 2013 at 10:19 AM, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > The package is extensible to the point that you could simply create a new > type of report that is output as some wiki language, so it wouldn't be > necessary to fork or modify ReportingTools. If there are internal utilities > for generating data tables that might be usefully shared, they could be > exposed, or at least factored out for ":::" access. There are also tools like the ascii package that can output various R data types (including data.frames) in various formats (markdown/pandoc, asciidoc, rst, org, textile, txt2tags). Sean > On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro <xavier.depedro at="" vhir.org="">wrote: > >> Dear Josh & co.: >> >> Thanks for producing such a package, it looks promising indeed! >> >> I see that it uses jquery data tables, and the live filtering of the data >> is very fast (nice!). >> I have a few quick questions, after a quick review of your vignette and >> examples: >> >> Have you experienced any issues when the data set contained in the browser >> is very large (regardless that you set the browser to display just 10 >> records at a time; I understand that the whole data set is loaded in the >> browser)? >> >> And in my relaxed todo list (without hurries) I had the idea to create a >> similar package to produce wiki syntax for tables from R data frames, and >> to display png (or svg) images within pages to be displayed through wiki >> engines (with it's appropriated syntax for the wiki engine of interest). A >> few years ago I had to do that and I produced some custom function 'ad hoc' >> without releasing it (yet) in any R package. In our example, we run r >> scripts through Tiki (wiki) pages, through PluginR, but the output is >> either bare text (so far) or images (png or svg), and any modification is >> handled by R commands by hand. And a function to produce the "Fancy Tables" >> that Tiki can produce with "JQuery Sortable Tables" is needed ( >> http://doc.tiki.org/**PluginFancyTable<http: doc.tiki.org="" pluginfa="" ncytable="">). I foresee that maybe the datatable jquery plugin could be even better >> for that, since it contains pagination and live filtering, which can be >> very very handy!. >> >> And maybe you are open to receive improvements/extensions to your package >> to support other ways to produce the tables required for better integration >> for wiki engines such as Tiki? Or should I fork from your package? >> >> Thanks in advanced, and congratulations for the generic package that you >> created. >> >> Xavier >> >> >> On 11/01/13 00:49, Josh Kaminker wrote: >> >>> Hi all, >>> >>> We present a new R package, >>> ReportingTools<http: www.**bioconductor.org="" packages="" **devel="" bioc="" html="" *="">>> *ReportingTools.html<http: www.bioconductor.org="" packages="" devel="" bi="" oc="" html="" reportingtools.html=""> >>> >, >>> for transforming the output of various Bioconductor packages into >>> interactive web pages. We have found this package very useful in our >>> collaborations with both bench and other computational scientists. >>> Examples >>> and instructions for generating output using this package can be found >>> here: http://research-pub.gene.com/**ReportingTools/<http :="" research-pub.gene.com="" reportingtools=""/> >>> >>> With just three lines of user code, rich HTML documents can be generated >>> from the result objects produced by several standard Bioconductor packages >>> including edgeR, limma, GOstats, and GSEAlm. By default, ReportingTools >>> reports include hyperlinks to relevant external databases and are highly >>> interactive through the use of filtering and sorting options provided by >>> open source javascript libraries. Supporting javascript and css libraries >>> are included with all reports, allowing them to be examined on a local >>> computer without a network connection. Additionally, in-line graphics >>> have >>> been developed to accompany statistical results to allow convenient visual >>> inspection of underlying raw data. ReportingTools output is highly >>> customizable and this package can be used equally well to share results >>> from automated pipeline processes or individual customized analyses. >>> >>> We are very interested in receiving your feedback including feature >>> requests for this package. >>> >>> Best regards, >>> >>> Josh Kaminker >>> Melanie Huntley >>> Jason Hackney >>> Jessica Larson >>> Christina Chaivorapol >>> >>> >>> >> >> -- >> Xavier de Pedro Puente, Ph.D. >> Statistics and Bioinformatics Unit (UEB) >> High Technology Unit (UAT) >> Vall d'Hebron Research Institute (VHIR). Mediterranean Building >> Passeig de la Vall d'Hebron, 119-129 >> 08035 Barcelona. Catalonia. Spain >> Ph. +34 934894007 / Fax +34 934894015 >> xavier.depedro at vhir.org >> http://ueb.vhir.org >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.8 years ago by Sean Davis21k
And there's the SortableHTMLTables package which deals specifically with sortable data tables. Michael On Fri, Jan 11, 2013 at 8:03 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Fri, Jan 11, 2013 at 10:19 AM, Michael Lawrence > <lawrence.michael@gene.com> wrote: > > The package is extensible to the point that you could simply create a new > > type of report that is output as some wiki language, so it wouldn't be > > necessary to fork or modify ReportingTools. If there are internal > utilities > > for generating data tables that might be usefully shared, they could be > > exposed, or at least factored out for ":::" access. > > There are also tools like the ascii package that can output various R > data types (including data.frames) in various formats > (markdown/pandoc, asciidoc, rst, org, textile, txt2tags). > > Sean > > > > On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro < > xavier.depedro@vhir.org>wrote: > > > >> Dear Josh & co.: > >> > >> Thanks for producing such a package, it looks promising indeed! > >> > >> I see that it uses jquery data tables, and the live filtering of the > data > >> is very fast (nice!). > >> I have a few quick questions, after a quick review of your vignette and > >> examples: > >> > >> Have you experienced any issues when the data set contained in the > browser > >> is very large (regardless that you set the browser to display just 10 > >> records at a time; I understand that the whole data set is loaded in the > >> browser)? > >> > >> And in my relaxed todo list (without hurries) I had the idea to create a > >> similar package to produce wiki syntax for tables from R data frames, > and > >> to display png (or svg) images within pages to be displayed through wiki > >> engines (with it's appropriated syntax for the wiki engine of > interest). A > >> few years ago I had to do that and I produced some custom function 'ad > hoc' > >> without releasing it (yet) in any R package. In our example, we run r > >> scripts through Tiki (wiki) pages, through PluginR, but the output is > >> either bare text (so far) or images (png or svg), and any modification > is > >> handled by R commands by hand. And a function to produce the "Fancy > Tables" > >> that Tiki can produce with "JQuery Sortable Tables" is needed ( > >> http://doc.tiki.org/**PluginFancyTable< > http://doc.tiki.org/PluginFancyTable>). I foresee that maybe the > datatable jquery plugin could be even better > >> for that, since it contains pagination and live filtering, which can be > >> very very handy!. > >> > >> And maybe you are open to receive improvements/extensions to your > package > >> to support other ways to produce the tables required for better > integration > >> for wiki engines such as Tiki? Or should I fork from your package? > >> > >> Thanks in advanced, and congratulations for the generic package that you > >> created. > >> > >> Xavier > >> > >> > >> On 11/01/13 00:49, Josh Kaminker wrote: > >> > >>> Hi all, > >>> > >>> We present a new R package, > >>> ReportingTools<http: www.**=""> bioconductor.org/packages/**devel/bioc/html/* > >>> *ReportingTools.html< > http://www.bioconductor.org/packages/devel/bioc/html/ReportingTools. html> > >>> >, > >>> for transforming the output of various Bioconductor packages into > >>> interactive web pages. We have found this package very useful in our > >>> collaborations with both bench and other computational scientists. > >>> Examples > >>> and instructions for generating output using this package can be found > >>> here: http://research-pub.gene.com/**ReportingTools/< > http://research-pub.gene.com/ReportingTools/> > >>> > >>> With just three lines of user code, rich HTML documents can be > generated > >>> from the result objects produced by several standard Bioconductor > packages > >>> including edgeR, limma, GOstats, and GSEAlm. By default, > ReportingTools > >>> reports include hyperlinks to relevant external databases and are > highly > >>> interactive through the use of filtering and sorting options provided > by > >>> open source javascript libraries. Supporting javascript and css > libraries > >>> are included with all reports, allowing them to be examined on a local > >>> computer without a network connection. Additionally, in-line graphics > >>> have > >>> been developed to accompany statistical results to allow convenient > visual > >>> inspection of underlying raw data. ReportingTools output is highly > >>> customizable and this package can be used equally well to share results > >>> from automated pipeline processes or individual customized analyses. > >>> > >>> We are very interested in receiving your feedback including feature > >>> requests for this package. > >>> > >>> Best regards, > >>> > >>> Josh Kaminker > >>> Melanie Huntley > >>> Jason Hackney > >>> Jessica Larson > >>> Christina Chaivorapol > >>> > >>> > >>> > >> > >> -- > >> Xavier de Pedro Puente, Ph.D. > >> Statistics and Bioinformatics Unit (UEB) > >> High Technology Unit (UAT) > >> Vall d'Hebron Research Institute (VHIR). Mediterranean Building > >> Passeig de la Vall d'Hebron, 119-129 > >> 08035 Barcelona. Catalonia. Spain > >> Ph. +34 934894007 / Fax +34 934894015 > >> xavier.depedro@vhir.org > >> http://ueb.vhir.org > >> > >> > >> ______________________________**_________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/**listinfo/bioconductor< > https://stat.ethz.ch/mailman/listinfo/bioconductor> > >> Search the archives: http://news.gmane.org/gmane.** > >> science.biology.informatics.**conductor< > http://news.gmane.org/gmane.science.biology.informatics.conductor> > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 6.8 years ago by Michael Lawrence11k
Ok, thanks for teh clarifications, Michael. Xavier On 11/01/13 16:19, Michael Lawrence wrote: > The package is extensible to the point that you could simply create a > new type of report that is output as some wiki language, so it > wouldn't be necessary to fork or modify ReportingTools. If there are > internal utilities for generating data tables that might be usefully > shared, they could be exposed, or at least factored out for ":::" access. > > Michael > > > On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro > <xavier.depedro@vhir.org <mailto:xavier.depedro@vhir.org="">> wrote: > > Dear Josh & co.: > > Thanks for producing such a package, it looks promising indeed! > > I see that it uses jquery data tables, and the live filtering of > the data is very fast (nice!). > I have a few quick questions, after a quick review of your > vignette and examples: > > Have you experienced any issues when the data set contained in the > browser is very large (regardless that you set the browser to > display just 10 records at a time; I understand that the whole > data set is loaded in the browser)? > > And in my relaxed todo list (without hurries) I had the idea to > create a similar package to produce wiki syntax for tables from R > data frames, and to display png (or svg) images within pages to be > displayed through wiki engines (with it's appropriated syntax for > the wiki engine of interest). A few years ago I had to do that and > I produced some custom function 'ad hoc' without releasing it > (yet) in any R package. In our example, we run r scripts through > Tiki (wiki) pages, through PluginR, but the output is either bare > text (so far) or images (png or svg), and any modification is > handled by R commands by hand. And a function to produce the > "Fancy Tables" that Tiki can produce with "JQuery Sortable Tables" > is needed ( http://doc.tiki.org/PluginFancyTable ). I foresee that > maybe the datatable jquery plugin could be even better for that, > since it contains pagination and live filtering, which can be very > very handy!. > > And maybe you are open to receive improvements/extensions to your > package to support other ways to produce the tables required for > better integration for wiki engines such as Tiki? Or should I fork > from your package? > > Thanks in advanced, and congratulations for the generic package > that you created. > > Xavier > > > On 11/01/13 00:49, Josh Kaminker wrote: > > Hi all, > > We present a new R package, > ReportingTools<http: www.bioconductor.org="" packages="" devel="" bi="" oc="" html="" reportingtools.html="">, > for transforming the output of various Bioconductor packages into > interactive web pages. We have found this package very useful > in our > collaborations with both bench and other computational > scientists. Examples > and instructions for generating output using this package can > be found > here: http://research-pub.gene.com/ReportingTools/ > > With just three lines of user code, rich HTML documents can be > generated > from the result objects produced by several standard > Bioconductor packages > including edgeR, limma, GOstats, and GSEAlm. By default, > ReportingTools > reports include hyperlinks to relevant external databases and > are highly > interactive through the use of filtering and sorting options > provided by > open source javascript libraries. Supporting javascript and > css libraries > are included with all reports, allowing them to be examined on > a local > computer without a network connection. Additionally, in- line > graphics have > been developed to accompany statistical results to allow > convenient visual > inspection of underlying raw data. ReportingTools output is > highly > customizable and this package can be used equally well to > share results > from automated pipeline processes or individual customized > analyses. > > We are very interested in receiving your feedback including > feature > requests for this package. > > Best regards, > > Josh Kaminker > Melanie Huntley > Jason Hackney > Jessica Larson > Christina Chaivorapol > > > > > -- > Xavier de Pedro Puente, Ph.D. > Statistics and Bioinformatics Unit (UEB) > High Technology Unit (UAT) > Vall d'Hebron Research Institute (VHIR). Mediterranean Building > Passeig de la Vall d'Hebron, 119-129 > 08035 Barcelona. Catalonia. Spain > Ph. +34 934894007 <tel:%2b34%20934894007> / Fax +34 934894015 > <tel:%2b34%20934894015> > xavier.depedro@vhir.org <mailto:xavier.depedro@vhir.org> > http://ueb.vhir.org > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
ADD REPLYlink written 6.8 years ago by Xavier de Pedro50
Answer: new package for generating interactive HTML reports
0
gravatar for Malcolm Cook
6.8 years ago by
Malcolm Cook1.5k
United States
Malcolm Cook1.5k wrote:
Michael, Glad to oblige. Assuming you already know org-mode/emacs.... * install DataTables from http://datatables.net/ in /some/useful/place/js/DataTables * put this in the 1st line of your .org file: # -*- org- export-babel-evaluate: nil; org-export-allow-BIND: t -*- * put another line in your .org file like this: #+SETUPFILE: "/some/useful/place/org/SETUPFILE.org" * put the following text in /some/useful/place/org/SETUPFILE.org : ###################################################################### ########## ## Making all org exported tables be, by default, ## sortable/filterable/pagable/... ## NOTE: #+BIND requires, to avoid prompting on each export, that ## org-export-allow-BIND be t, as is indicated to emacs with "-*- modeline ; org-export-allow-BIND: t -*-" ## Something to do with security ;) ###################################################################### ########## #+BIND: org-export-html-table-tag "" #+STYLE: <script type="text/javascript" charset="utf8" src="/some/useful/place/js/DataTables/media/js/jquery.js"></script> #+STYLE: <link rel="stylesheet" type="text/css" href="/some/usef ul/place/js/DataTables/media/css/jquery.dataTables.css"></script> #+STYLE: <script type="text/javascript" charset="utf8" src="/some/usef ul/place/js/DataTables/media/js/jquery.dataTables.min.js"></script> #+STYLE: <script type="text/javascript" charset="utf8" src="/some/usef ul/place/js/DataTables/extras/TableTools/media/js/TableTools.min.js">< /script> #+STYLE: <script type="text/javascript">$(document).ready(function(){$ ('.dataTable').dataTable({"sPaginationType": "full_numbers","sScrollX": "100%", "bStateSave": true, "bProcessing": true, "bDeferRender": true, "aaSorting": [] , "sDom": 'ClifrtrpT<"afterTable">', "oTableTools": { "sSwfPath": "/some/useful/ place/js/DataTables/extras/TableTools/media/swf/copy_csv_xls.swf"}}); $("div.afterTable").html('
');});</script> Your paths may vary. These worked at the time of deployment a few months ago. To have DataTable sort on p-values and other scientific notation, put another line in our SETUPFILE.org: #+STYLE: <script type="text/javascript" src="/some/useful/place/js/myDatatableUtil.js"></script> ...and put the following in that file: jQuery.fn.dataTableExt.aTypes.unshift( function ( sData ) { if (! isNaN(parseFloat(sData))) { return 'scientific'; } return null; } ); jQuery.extend( jQuery.fn.dataTableExt.oSort, { "scientific-pre": function ( a ) { return parseFloat(a); }, "scientific-asc": function ( a, b ) { return ((a < b || isNaN(a)) ? -1 : ((a > b || isNaN(b)) ? 1 : 0)); }, "scientific-desc": function ( a, b ) { return ((a < b || isNaN(a)) ? 1 : ((a > b || isNaN(b)) ? -1 : 0)); } } ); ~Malcolm From: Michael Lawrence [mailto:lawrence.michael@gene.com] Sent: Friday, January 11, 2013 3:11 PM To: Cook, Malcolm Subject: Re: [BioC] new package for generating interactive HTML reports Hi Malcolm, That sounds really cool. Mind passing me the magic style options? Or a URL? Thanks, Michael On Fri, Jan 11, 2013 at 12:13 PM, Cook, Malcolm <mec@stowers.org<mailto:mec@stowers.org>> wrote: Melanie, I too have employed the jsQuery dataTable. I use emacs org mode to generate reports with embedded tables, all of which are made indiscriminately made scrollable/pageable/searchable with the inclusion of a few style directives in the org file. With the same upsides&downsides you are discussing here. I recommend it for simple standalone html non-interactive reporting. In my experience, tens of thousands of rows are easily handled on chrome browser on local area network. ~Malcolm .-----Original Message----- .From: bioconductor-bounces@r-project.org<mailto:bioconductor- bounces@r-project.org=""> [mailto:bioconductor- bounces@r-project.org<mailto:bioconductor-bounces@r-project.org>] On Behalf Of Melanie Huntley .Sent: Friday, January 11, 2013 12:37 PM .To: Sean Davis .Cc: Josh Kaminker; Michael Lawrence; Melanie Huntley; bioconductor@r-project.org<mailto:bioconductor@r-project.org> .Subject: Re: [BioC] new package for generating interactive HTML reports . .Hi Sean, . .There certainly seem to be more available options to speed things up if we .require the hard work to be done server side - we were considering this in .the initial phases of the package devel. . .Our thinking was to keep things as user friendly as possible to start (ie. .keep things client side) - but the trade-off has been a decrease in .responsiveness for very large datasets. Perhaps we should revisit the .server option again for the next release if we don't find a client side .solution. . .Thanks, .Melanie . .On Fri, Jan 11, 2013 at 10:23 AM, Sean Davis <sdavis2@mail.nih.gov<mailto:sdavis2@mail.nih.gov>> wrote: . .> .> Hi, Melanie. .> .> The "extra" scroller for datatables allows scrolling of VERY large .> datasets because only a small portion of the entire dataset is sent to .> the client at one time. The server simply responds to requests for .> data as the dataset scrolls on the client. The details are here: .> .> .> http://datatables.net/release-datatables/extras/Scroller/server- side_processing.html .> .> This would require a server that responds to queries be running while .> the client is interacting with the data. .> .> Sean .> .> .> .> > On Fri, Jan 11, 2013 at 7:19 AM, Michael Lawrence < .> lawrence.michael@gene.com<mailto:lawrence.michael@gene.com> .> >> wrote: .> > .> >> The package is extensible to the point that you could simply create a .> new .> >> type of report that is output as some wiki language, so it wouldn't be .> >> necessary to fork or modify ReportingTools. If there are internal .> utilities .> >> for generating data tables that might be usefully shared, they could be .> >> exposed, or at least factored out for ":::" access. .> >> .> >> Michael .> >> .> >> .> >> On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro < .> xavier.depedro@vhir.org<mailto:xavier.depedro@vhir.org> .> >> >wrote: .> >> .> >> > Dear Josh & co.: .> >> > .> >> > Thanks for producing such a package, it looks promising indeed! .> >> > .> >> > I see that it uses jquery data tables, and the live filtering of the .> data .> >> > is very fast (nice!). .> >> > I have a few quick questions, after a quick review of your vignette .> and .> >> > examples: .> >> > .> >> > Have you experienced any issues when the data set contained in the .> >> browser .> >> > is very large (regardless that you set the browser to display just 10 .> >> > records at a time; I understand that the whole data set is loaded in .> the .> >> > browser)? .> >> > .> >> > And in my relaxed todo list (without hurries) I had the idea to .> create a .> >> > similar package to produce wiki syntax for tables from R data frames, .> and .> >> > to display png (or svg) images within pages to be displayed through .> wiki .> >> > engines (with it's appropriated syntax for the wiki engine of .> interest). .> >> A .> >> > few years ago I had to do that and I produced some custom function 'ad .> >> hoc' .> >> > without releasing it (yet) in any R package. In our example, we run r .> >> > scripts through Tiki (wiki) pages, through PluginR, but the output is .> >> > either bare text (so far) or images (png or svg), and any .> modification is .> >> > handled by R commands by hand. And a function to produce the "Fancy .> >> Tables" .> >> > that Tiki can produce with "JQuery Sortable Tables" is needed ( .> >> > http://doc.tiki.org/**PluginFancyTable< .> >> http://doc.tiki.org/PluginFancyTable>). I foresee that maybe the .> >> datatable jquery plugin could be even better .> >> > for that, since it contains pagination and live filtering, which can .> be .> >> > very very handy!. .> >> > .> >> > And maybe you are open to receive improvements/extensions to your .> package .> >> > to support other ways to produce the tables required for better .> >> integration .> >> > for wiki engines such as Tiki? Or should I fork from your package? .> >> > .> >> > Thanks in advanced, and congratulations for the generic package that .> you .> >> > created. .> >> > .> >> > Xavier .> >> > .> >> > .> >> > On 11/01/13 00:49, Josh Kaminker wrote: .> >> > .> >> >> Hi all, .> >> >> .> >> >> We present a new R package, .> >> >> ReportingTools<http: www.**="" .=""> >> bioconductor.org/packages/**devel/bioc/html/*<http: bioconduct="" or.org="" packages="" **devel="" bioc="" html="" *=""> .> >> >> *ReportingTools.html< .> >> .> http://www.bioconductor.org/packages/devel/bioc/html/ReportingTool s.html> .> >> >> >, .> >> >> for transforming the output of various Bioconductor packages into .> >> >> interactive web pages. We have found this package very useful in our .> >> >> collaborations with both bench and other computational scientists. .> >> >> Examples .> >> >> and instructions for generating output using this package can be .> found .> >> >> here: http://research-pub.gene.com/**ReportingTools/< .> >> http://research-pub.gene.com/ReportingTools/> .> >> >> .> >> >> With just three lines of user code, rich HTML documents can be .> generated .> >> >> from the result objects produced by several standard Bioconductor .> >> packages .> >> >> including edgeR, limma, GOstats, and GSEAlm. By default, .> ReportingTools .> >> >> reports include hyperlinks to relevant external databases and are .> highly .> >> >> interactive through the use of filtering and sorting options .> provided by .> >> >> open source javascript libraries. Supporting javascript and css .> >> libraries .> >> >> are included with all reports, allowing them to be examined on a .> local .> >> >> computer without a network connection. Additionally, in- line .> graphics .> >> >> have .> >> >> been developed to accompany statistical results to allow convenient .> >> visual .> >> >> inspection of underlying raw data. ReportingTools output is highly .> >> >> customizable and this package can be used equally well to share .> results .> >> >> from automated pipeline processes or individual customized analyses. .> >> >> .> >> >> We are very interested in receiving your feedback including feature .> >> >> requests for this package. .> >> >> .> >> >> Best regards, .> >> >> .> >> >> Josh Kaminker .> >> >> Melanie Huntley .> >> >> Jason Hackney .> >> >> Jessica Larson .> >> >> Christina Chaivorapol .> >> >> .> >> >> .> >> >> .> >> > .> >> > -- .> >> > Xavier de Pedro Puente, Ph.D. .> >> > Statistics and Bioinformatics Unit (UEB) .> >> > High Technology Unit (UAT) .> >> > Vall d'Hebron Research Institute (VHIR). Mediterranean Building .> >> > Passeig de la Vall d'Hebron, 119-129 .> >> > 08035 Barcelona. Catalonia. Spain .> >> > Ph. +34 934894007<tel:%2b34%20934894007> / Fax +34 934894015<tel:%2b34%20934894015> .> >> > xavier.depedro@vhir.org<mailto:xavier.depedro@vhir.org> .> >> > http://ueb.vhir.org .> >> > .> >> > .> >> > ______________________________**_________________ .> >> > Bioconductor mailing list .> >> > Bioconductor@r-project.org<mailto:bioconductor@r-project.org> .> >> > https://stat.ethz.ch/mailman/**listinfo/bioconductor< .> >> https://stat.ethz.ch/mailman/listinfo/bioconductor> .> >> > Search the archives: http://news.gmane.org/gmane.** .> >> > science.biology.informatics.**conductor< .> >> http://news.gmane.org/gmane.science.biology.informatics.conductor> .> >> > .> >> .> >> [[alternative HTML version deleted]] .> >> .> >> _______________________________________________ .> >> Bioconductor mailing list .> >> Bioconductor@r-project.org<mailto:bioconductor@r-project.org> .> >> https://stat.ethz.ch/mailman/listinfo/bioconductor .> >> Search the archives: .> >> http://news.gmane.org/gmane.science.biology.informatics.conductor .> >> .> > .> > .> > .> > -- .> > Melanie Huntley, Ph.D .> > Bioinformatics and Computational Biology .> > Genentech, Inc. .> > huntley.melanie@gene.com<mailto:huntley.melanie@gene.com> .> > .> > [[alternative HTML version deleted]] .> > .> > _______________________________________________ .> > Bioconductor mailing list .> > Bioconductor@r-project.org<mailto:bioconductor@r-project.org> .> > https://stat.ethz.ch/mailman/listinfo/bioconductor .> > Search the archives: .> http://news.gmane.org/gmane.science.biology.informatics.conductor .> . . . .-- .Melanie Huntley, Ph.D .Bioinformatics and Computational Biology .Genentech, Inc. .huntley.melanie@gene.com<mailto:huntley.melanie@gene.com> . . [[alternative HTML version deleted]] . ._______________________________________________ .Bioconductor mailing list .Bioconductor@r-project.org<mailto:bioconductor@r-project.org> .https://stat.ethz.ch/mailman/listinfo/bioconductor .Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENTlink written 6.8 years ago by Malcolm Cook1.5k
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