12,100 results • Page 1 of 202
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 3 Sep 2004 - affy: N…
updated 21.3 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only.</div
updated 22.5 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only.</div
updated 21.5 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 30 April 2004: annaff…
updated 21.6 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 08/06/2004 The bug…
updated 21.4 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 7 April 2004: limma 1…
updated 21.7 years ago • madman@jimmy.harvard.edu
<div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 04 March 2004: PROc…
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - July 30, 2003 - Metad…
updated 22.4 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 28 June 2004: limma …
updated 21.4 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - Oct. 31 2003: metaDat…
updated 22.1 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 5 July 2003: limma - …
updated 22.5 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 6 Dec 2003: limma 1.3…
updated 22.0 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 2 October 2003: limma…
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 05 Feb 2004: reposToo…
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...REL1.1 and Devel) - JG Apr 29 2003: annotate - references to data package hgu95a have been changed to hgu95av2. JG Apr 29 2003: limma - imported version 1.0.2 - fixed bug in ebaye…
<div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 06 September 2003: …
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 30 Dec 2003: limma 1.…
updated 21.9 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history
if I type a function name in R, it'll print the function for me. Unfortunately, it does so without comments. Is there a way to get the function with comments? A related question: how can I access the documentation/comments for
updated 17.5 years ago • Arkady
div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the files madman/Rpacks/NEWS and NEWS.old at any time for up to date information...Also, please remember to edit the NEWS file yourself after making any noteworthy changes to the packages - follow the format used in these files and make sure to sign your name to …
want to run an idea past this list as a sanity check. I would especially value Gordon and Charity's comments if they have time. The voom log transformation is essentially: log2( (count+0.5) / library.size ) It then does some clever...weighting low counts, I'm trying to get rid of the extra variation from low counts by artificially left censoring the data. - I'm using the mean of the libaray…
updated 12.9 years ago • Paul Harrison
Is there a way to retrieve history for specific packages? For example, even basic information such as when which version was released
updated 10.5 years ago • igor
to 1.0.3 in the release version of Biconductor (2.5). This fixes a broken build caused by the recent update of DBI on CRAN. BUG FIXES o The recently release of DBI version 0.2-5 on CRAN fixed a name mangling bug whereby a...column name of "end" would silently be changed to "end__1". This columnname was used internally in Genominator so a change was warranted. Genominator now depends...…
updated 16.0 years ago • Kasper Daniel Hansen
div class="preformatted">Dear list: On the Windows version one can bring back R command history at the prompt by using a up-ward arrow key. Unfortunately I can not do the same thing on a Sun unix machine. I am wondering...if one can set up the history function or command editing function, what ever you call that, with the unix version of R? Thanks in advance! Jianping
updated 19.6 years ago • Jianping Jin
Hi Matt and Nadia, For almost a year, I was using goseq as a generalized enrichment tool (leveraging the gene length bias correction implemented there, thank you) using my custom gene sets this way: goseq(myData, genome=NULL, id=NULL, gene2cat = MyVeryOwnGeneCategorization, method="Sampling", repcnt = 100000) After recent update to version 1.18.0, the pipeline crashed and return…
updated 10.9 years ago • Oleg Moskvin
the changes in expression not explained by the cell counts (either because they come from cell types not included in the model...or because they come from free RNA in plasma). We also want to explain the changes in expression associated with each blood cell. ### Data - Expression values before and after the race extracted from...and platelets). - Some possible confounding variables (age,…
Is there a simple way to get comments from a VCF header of a VCF object? For example, consider the following excerpt of a VCF file: ##contig= <id=hla-drb1*15:03...Is there a simple way to get comments from a VCF header of a VCF object? For example, consider the following excerpt of a VCF file: ##contig= <id=hla-drb1*15:03:01...positives with a list of failed filters and true…
updated 5.5 years ago • Dario Strbenac
div class="preformatted">What follows is some random comments on the use of GRanges for storing data in the elementMetadata slot. My use case is a lot of very small ranges (&gt;10M...but very important to me :). I am particular interested in fast subsetting like subsetByOverlaps. Comments: * I find column subsetting on the elementMetadata to be really slow, slower than it need to be I …
updated 15.3 years ago • Kasper Daniel Hansen
to run an idea past this list as a sanity check. I would &gt; especially value Gordon and Charity's comments if they have time. &gt; &gt; The voom log transformation is essentially: &gt; &gt; log2( (count+0.5) / library.size ) &gt; &gt; It then...low counts, I'm trying to get rid of the &gt; extra variation from low counts by artificially left censoring the &g…
updated 12.9 years ago • Wolfgang Huber
automatically test BioConductor packages. As a package developer, how can I upload the experimental source version of a package to get test results from a specific test server? **Use case:** Our package contains an error that started...to appear only recently and only on Windows systems. The *tokay1* server of checkResults documented the error in our latest BioConductor...version. I would like…
updated 5.2 years ago • p.stahlhofen
div class="preformatted">Hi Lana, The MSigDB is a good source! We are planning to have a summer student working on a similar project, but using a different database. Maybe we can coordinate...Mon, 12 Mar 2007 14:39:54 -0700 From: "Lana Schaffer" <schaffer@scripps.edu> Subject: Re: [BioC] Category To: <bioconductor at="" stat.math.ethz.ch=""> Message-ID: &lt;016001c764ee$f92bf…
updated 18.8 years ago • Simon Lin
treatments, with three replicate individuals each. The species fall into three physiological categories. I would like to identify genes whose response to the treatments varies by physiological category.&nbsp; I think...as independent (I get apparently sensible results given prior knowledge) but we know from a long history of work in comparative methods that they are not, and I am concerned t…
div class="preformatted">Hi all, I recently came across a paper (Maria Chahrour, et al. MeCP2, a Key Contributor to Neurological Disease, Activates and Represses...Figure S1 which basically plots cellular component, biological process, and molecular function categories that differ significantly based on on genes that are differentially expressed in two conditions. I wonder whether
updated 17.6 years ago • affy snp
<div class="preformatted">Dear list, I have a theoretical question regarding Filtering on Variation in the Category package. I've performed an analysis that closely resembles the Vignette, but I am still a bit uncertain about the filtering. In the Vignette the following code is used: lowQ&lt;-rowQ(eset,floor(0.25*NumArrays)) upQ&lt;-rowQ(eset,ceiling(0.75*NumArrays)) iqrs&lt;-u…
updated 18.4 years ago • Boel Brynedal
groups in my data. The metadata are TCGA-LGG samples and I am interested in phenotype of seizure history. The two groups I am interested in are 177 samples in no seizure history group and 298 samples in yes seizure history...each individual. For example, if I have a gene set 'calcium signaling pathway' enriched in seizure history yes group, I would like to take one individual from the group, calc…
updated 8.4 years ago • sup230
everybody, I was wondering whether there is a package to cluster a list of genes to different GO categories my problem is as such: i have a list of genes (a tab delimited file): id flybasename_gene flybase_gene_id entrezgene...FBgn0034454 37248 protein binding I would like to try and group the genes in various GO categories, which are mentioned here in the last columns. The GO c…
updated 15.0 years ago • Assa Yeroslaviz
I'm troubled because what looks like the same object behaves very differently depending on my "history." With a clean history (.Rhistory and .Rdata deleted), I get this: &gt; library("genefilter") &gt; data(sample.ExpressionSet) &gt...others like it) work: &gt; varLabels(eset) [1] "sex" "type" "score" But if I now quit and save history, then start again and go: &gt;…
updated 18.2 years ago • Thomas Elliott
I can't change the y-axis' category order of dotplot result, I don't know the default order of it. I've used ordrBy="x",orderBy="Count",orderBy...I can't change the y-axis' category order of dotplot result, I don't know the default order of it. I've used ordrBy="x",orderBy="Count",orderBy="geneRatio" in dotplot() parameters, but nothing changed. Thank you very much! ``` #ego &lt;- enric…
updated 4.2 years ago • Yang
it loads properly. I get the following error output, however, when I try to run hyperGTest, package Category, on a vector of Entrez Gene IDs and a vector of the gene universe of the chip. I suspect I did something wrong when building...0.05, conditional = TRUE, testDirection = "over") &gt; params A GOHyperGParams instance category: GO annotation: ragene10stv1 &gt; hyperGTest(params) Err…
Hi all, I have a good amount of experience in doing differential gene expression analysis in two categories like healthy samples and disease patients. Now I have three categories of patients at baseline, then at week 16...and week 52. I am thinking to try one way anova on this data. Any information on links or any good sources of DE analysis with anova&nbsp;awould be really appreciated.&…
updated 8.5 years ago • pbachali
the licensing policy of Bioconductor. According to <http://www.bioconductor.org/about/>, the open source policy is: * __Open source__. The Bioconductor project has a commitment to full open source discipline, with distribution...via a public subversion (version control) server. All contributions exist under an open source license such as Artistic 2.0, GPL2, or BSD. There are many differe…
updated 8.6 years ago • zeehio
Dear all, I have some gene expression data sets. In some of the data sets, I am comparing two age categories, and in some I am comparing multiple age categories. For each dataset, I want to do a two-tailed F test between the age...correctly. If someone had the time to glance at the code below and edit the line that I should change, so that the code reads: I input the pData (different age catego…
updated 9.1 years ago • StephK
expression (lmFit and eBayes). I get a high number of DE genes. Most of these belong to Category: Main. However, some of them, belongs to other categories such as normgene-&gt;intron, control-&gt;affx, normgene-&gt;exon...As I understand it, empirical Bayes takes into consideration the full data set. Removing all other categories, some of them which are not supposed to be changed bet…
updated 13.4 years ago • Martin O'Hare
Hi, I'm trying to use the `gate_mindensity2` from the openCyto package to gate out debris from my .fcs files. I'm using https://flowrepository.org/id/FR-FCM-ZZ36 as an example. I can gate out the debris at the lower end (i.e. left hand side of the gate) but if I want to apply a gate to remove the events on the right hand side, I am unable to do so, even if I set the `positive` argument to TR…
updated 6.9 years ago • biomiha
<div class="preformatted">Dear Bioconductor List, I have just installed R version 2.15.2 on a Mac running under Mac OS X 10.7.5. I want to install the development version of Bioconductor so that I can access and install the development version of easyRNASeq. Here is my session record: version 2.15.2 (2012-10-26) -- "Trick or Treat" Copyright (C) 2012 The R Foundation for Statisti…
updated 13.1 years ago • Richard Friedman
I am using goseq for category testing of differentially expressed genes in my RNA-seq data sets and I wanted to extend it to categories other than...the GO categories. Specifically, I wanted to make use of the molecular signatures database (MSigDB). To be clear, I am not trying to do...a ranking approach like GSEA. I would simply like to take advantage of the extensive list of categories in MSigD…
updated 7.3 years ago • Mthabisi Moyo
div class="preformatted">Hi, I am having troubles with cateGOry as follows: &gt; m &lt;- cateGOry(go$refseq_dna, go$go, FALSE) Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442...Neither worked. Any idea? Thanks, Oleg &gt; index &lt;- c(24, 172, 1978, 1979, 4441) &gt; m &lt;- cateGOry(go$refseq_dna[-index], go$go[-index], FALSE) Error in augment…
updated 18.6 years ago • Oleg Sklyar
How do I add ME labels (ex. MEcyan) to the left hand side of my eigengene adjacency heatmap? I’ve seen this figure produced in publications. Is there an argument for...How do I add ME labels (ex. MEcyan) to the left hand side of my eigengene adjacency heatmap? I’ve seen this figure produced in publications. Is there an argument for the...setMargins=TRUE, plotHeatmaps=TRUE, plotDendrograms=FALSE) …
updated 6.2 years ago • normingt
This is a request for comments on planned changes to the ensemblVEP package. The intent is to provide lightweight wrappers to the ensembl VEP REST...API and to deprecate most of the software in the package. Users of ensemblVEP may respond with comments to this post to describe their use cases. As examples of new approaches emerge in development, I will post more details
updated 24 months ago • Vincent J. Carey, Jr.
go to http://www.bioconductor.org/help/course-materials/ (also accessible from our home page as the "Recent courses" link in the "Learn" box) Courses are searchable and sortable by keyword, course name, title, date, and more. Thanks...to everyone who attended BioC2014 and gave us feedback which prompted this change. Dan
updated 11.3 years ago • Dan Tenenbaum
<div class="preformatted">Hello bioC users, as you can see below, this was posted over a year ago. Unfortunately I tried the same today and for some mysterious it is not working correctly any more. What I have is the same data.frame: &gt; dat id flybasename_gene flybase_gene_id entrezgene 1 1616608_a_at Gpdh FBgn0001128 33824 2 1622892_s_at CG3…
updated 13.4 years ago • Assa Yeroslaviz
div class="preformatted">Hello, I was wondering whether anyone could suggest sources of information about amplified genes in cancer, especially if the website tries to combine it with (over)expression...information. We wrote a review on amplified and expressed genes recently and are trying to get a sense of what else is out there, so that when we update it we make sure we get different sourc…
updated 15.3 years ago • Daniel Brewer
builds[index], sep = ""), : unable to open connection Is it because that GO has changed its downloading address from: "http://www.godatabase.org/dev/database/archive/latest" to "http://archive.godatabase.org
updated 20.5 years ago • JUNHAI GUO
the best way to proceed in this case. "Level1" individuals become "level2" individuals because they change behavior throughout their lifespan. Perhaps that "level2" individual had very recently transitioned from "level1...that "level2" individual as "level1", or perhaps consider "level1 + level2" individuals as a single category and compare against "level3", since I'm mostly interested in the gen…
updated 7.5 years ago • fl
I had written to do GO analysis using the package GOstats, and to do this by switching to package Category. I wanted to add KEGG testing to the GO testing I have been doing. All I did to my code was to add a conditional such that...if the category was KEGG a KEGGHyperGParams object would be created, else if it was BP, MF, or CC a GOHyperGParams object would be created...Then the object params wou…
div class="preformatted">Hi, Instead of using GO or KEGG categories, is it possible to use customerized categories. For example: CC1 : gene1, gene2, gene3 CC2 : gene4, gene5.. instead of GO1...gene1, gene2 I am just wondering which package allows me to give my own defn. of categories. For this purpose, I made a code from basic Hypergeometric {stats} by using dhyper. But what I got is prob…
updated 19.0 years ago • Weiwei Shi
<div class="preformatted">Dear List I want to do a hypergeometric testing of GO, KEGG and PFAM terms. I'm using the GOstats package and the method described in the vignette: "How to use GOstas and Category to do hypergeometric testing with unsupported model organisms" by M. Carlson, Oct. 31. 2011, because my organism is a...I'm using the GOstats package and the method described in the vign…
shorter lines; 501 lines (14%) are &gt; 80 characters long. Most of these lines are roxygen comments. formatR package says : &gt; Also note that single lines of long comments will be wrapped into &gt; shorter ones automatically...when wrap = TRUE, but roxygen comments will &gt; not be wrapped (i.e., comments that begin with #'). Don't tell me I have to do this one l…
updated 4.3 years ago • ZheFrench
numbers of genes per GO category. __\#\#\# Approach 1 \#\#\#__ <pre> &gt; library(goseq) &gt; gene.vector = as.integer(assayed.genes%in%de.genes) #19,792 total genes (502...bosTau4", "ensGene") &gt; GO.hiper = goseq(pwf, "bosTau4", "ensGene") &gt; GO.hiper[GO.hiper$category=="GO:0005509",] category over_represented_pvalue under_represented_pvalue numDEInCat numI…
updated 7.6 years ago • frezende
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