Bioconductor Forum

The deadline to nominate a qualified candidate is May 31, 2021! Our awardees will be selected, each having contributed to the project in an outstanding way based on one or more of selection

Bioconductor Bioc2021 Recognition Awards

updated 4.5 years ago • shepherl

https://forms.gle/d9PyAjAw62yVKxjL8) to nominate someone. The deadline for nominations is May 31, 2021

Awards Recognition Bioconductor Bioc2021

updated 4.7 years ago • shepherl

div class="preformatted">Extended draft paper submission: BCBGC-09 call for papers This Extended Call for Papers for the 2009 International Conference on Bioinformatics...09) (website: http://www.PromoteResearch.org ) is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will...A…

updated 16.6 years ago • John Edward

div class="preformatted">some have asked me about pooling in microarrays. a paper by Kendziorski, et al can be found here http://www.bepress.com/jhubiostat/paper46/</div

updated 21.4 years ago • Rafael A. Irizarry

div class="preformatted">Dear all, The paper on IRanges, GenomicRanges and GenomicFeatures (Software for Computing and Annotating Genomic Ranges) has been published...through PLoS Computational Biology[1]. Please cite the paper whenever basing software on the infrastructure, or making direct use of it data analyses. A big thanks to the co-authors

Infrastructure IRanges GenomicFeatures GenomicRanges Infrastructure IRanges GenomicFeatures

updated 12.3 years ago • Michael Lawrence

I actually need to download pdfs through R code. The thing which I want to do is that, search for a paper in pubmed, which is possible by using GetPubMed function in the package "NCBI2R?". GetPubMed(searchterm, file = "", download...all hits, although if I go to the pubmed, I can download it. So, the problem is not that, for each paper I have to download the pdfs (which are available if I go to…

GO GO

updated 12.9 years ago • nooshin

Content-Disposition: attachment; filename="cfp-main.txt" InfoVis 2003 Call for Papers ---------------------------------------------------------------------- -- Changes ---------------------------------------------------------------------- -- New this year * InfoVis Contest, see http://www.cs.umd.edu/hcil/iv03contest * New paper categories (technique...to support the subm…

Visualization PROcess Category Visualization PROcess Category

updated 22.9 years ago • rgentleman

the reason for this email, is the ability to upload a 5-10 minute video describing your scientific paper. For one of our first examples see http://www.scivee.tv/node/53. We cannot tell you what will be the long term impact of making...for the short term (see http://www.scivee.tv/worth_it) indicates that it renews interest in your paper. It also adds a human element to the work which can be parti…

updated 18.2 years ago • Phil Bourne

div class="preformatted">I am looking for references to published papers on microarrays which mention duplicate spots, i.e., replicate spots on the same array containing the same probe. The...that log-ratios from duplicate spots were averaged before further analysis. I am particularly after papers in mainline biological journals. Any references would be much appreciated. Thanks a lot Gordon&l…

probe probe

updated 21.8 years ago • Gordon Smyth

<div class="preformatted">Dear all, Paper describing the mathematical details about tweeDEseq package has been published at BMC Bioinformatics http://www.biomedcentral.com/1471-2105/14/254/abstract The paper also compares the performance of tweeDEseq against edgeR and DESeq under a large number of scenarios. The results obtained...div class="preformatted">Dear all, Paper describing t…

edgeR tweeDEseq edgeR tweeDEseq

updated 12.3 years ago • Gonzalez Ruiz, Juan Ramon

IV07/IVbm.htm > ETH, Zurich, Switzerland > July 4, 2007 > > > *** Extended Paper deadline: 15 March, 2007 *** > > Associated and co-located with the 11th International Conference on Infor= mation Visualization...gt; July 4 - 6, 2007 > > CALL FOR PARTICIPATION > > We are soliciting original papers in the area of informati…

Microarray Alignment Pathways Visualization Microarray Alignment Pathways Visualization

updated 18.8 years ago • Vincent J. Carey, Jr.

in English. Paper registration and electronic submission will start in August 2006. Submitted papers will be carefully evaluated based...on originality, significance, technical soundness, and clarity of exposition. *Papers:* Please submit your paper as PDF file only. Paper submissions in LNCS format (http://www.springer.de/comp/lncs/authors.html...nor in figures. The submitted manuscript should…

Pathways microRNA Pathways microRNA

updated 19.2 years ago • Prof.Roland Wagner

https://biocasia2021.bioconductor.org/) On behalf of the BioC Asia 2021 Organising Committee, we very much looking forward to seeing you online

Workshop Asia BioCAsia Conference

updated 4.2 years ago • Peter Hickey

Once again, we received excellent applications to serve on the Community Advisory Board (CAB) in 2021. Nominations were voted upon by existing members of the CAB, and as a result of this process, we're pleased to welcome the

bioconductoroversight news community BiocVersion

updated 4.7 years ago • Matthew Ritchie

div class="preformatted">Does anyone know where to get R-Codes for Irizarry's Stochastic models paper? Thanks Stephen.</div

updated 21.6 years ago • Stephen Nyangoma

you to submit a manuscript for this session. All manuscripts will be peer-reviewed, and accepted papers will appear in both the bound and electronic online proceedings and will be indexed in PubMed. The paper submission

annotate annotate

updated 22.5 years ago • Wang, Hui

<div class="preformatted">I've had several requests for references to published papers in the biology literature using the limma package. There have been three articles appear since June that I know of: Golden...div class="preformatted">I've had several requests for references to published papers in the biology literature using the limma package. There have been three articles appear si…

Microarray limma Microarray limma

updated 21.3 years ago • Gordon Smyth

in English. Paper registration and electronic submission will start in August 2006. Submitted papers will be carefully evaluated based...on originality, significance, technical soundness, and clarity of exposition. *Papers:* Please submit your paper as PDF file only. Paper submissions in LNCS format (http://www.springer.de/comp/lncs/authors.html...nor in figures. The submitted manuscript should…

Pathways microRNA Pathways microRNA

updated 19.3 years ago • Prof.Roland Wagner

statistical methods for detecting differentially expressed genes from RNA-seq data this is a good paper to compare them but who can give more comparision ? -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University

updated 13.1 years ago • wang peter

USAR2009 R/R-PLUS/S CONFERENCE ANNOUNCEMENT & CALL FOR PAPERS ============================================================== The 2009 R/R-PLUS/S Conference will take place in Las Vegas,USA April 26-39, 2009 The meeting is open to all R/S-related users...welcome contributions on R/S-related topics from all fields, academic and professional. Submit your paper or poster abstract online. …

updated 17.1 years ago • sue@xlsolutions-corp.com

if anyone knew where the python module is to carry out pathway analysis using the methods in the paper by Kim and Volsky (2005) in their paper "PAGE: Parametric Analysis of Gene Set Enrichment paper"? It is not clear if they...produced a python module from the paper and if they did i have not been able to find it! Any help would be great to point me in the right direction Thanks Danie…

GSEA PAGE microarray differential gene expression pathway analysis

updated 8.7 years ago • danielle.newby

<div class="preformatted">2009 World Congress on Computer Science and Information Engineering (CSIE 2009) March 31 - April 2, 2009 Los Angeles/Anaheim, USA http://world-research-institutes.org/conferences/CSIE/2009 CALL FOR PAPERS, INVITED SESSIONS & EXPO The Los Angeles/Anaheim area is known for its many renowned attractions, such as Disneyland, Universal Studios and the Hollyw…

updated 17.2 years ago • Hongping Wu

packages* What should I do to load the airway package sessionInfo( ) *R version 4.1.2 (2021-11-01) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.1 Matrix products: default LAPACK: /Library

airway

updated 3.9 years ago • j.jacob1

Hi I am almost finished my package and the paper is nearly done too. Which order do I submit these in? Do I wait for it to be accepted by the bioconductor then submit to journal

bioconductor

updated 8.5 years ago • chris86

it successfully for a qPCR array with 96 genes. I was wondering if someone knows about a couple of papers where limma is used to assess DEGs in a qPCR array and not on another microarray platform or RNA seq. I know it's perfectly

limma

updated 7.4 years ago • Daniel Moreno

normalization and under-sampling of microbial communities on differential abundance detection. The paper: http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2658.html The package: http://bioconductor.org/packages

Normalization metagenomeSeq Normalization metagenomeSeq

updated 12.2 years ago • Hector Corrada Bravo

div class="preformatted">Draft paper submission deadline extended: BCBGC-09 The deadline for draft paper submission at the 2009 International Conference...the authors. The conference will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The conference will take place at the same time and venue where several other international conferences

updated 16.8 years ago • John Edward

also be held at the same time and place (each conference has its own proceedings). We invite draft paper submissions. See the website: http://www.iiconference.org for more details. Proceedings will be submitted for indexing

updated 12.8 years ago • Venkateswara Rao

div class="preformatted">Dear Dietmar, Thank you very much for the feedback of the paper and the package! Where did you download the package and what is the package version? It could be that the dataset was not...dfernandez045 at="" ikasle.ehu.es=""> wrote: > Dear Dr. Zhu, > > I have just read the paper you and your colleagues have written > "ChIPPeakAnno: a B…

Transcription ChIPSeq Annotation chipseq genomes Transcription ChIPSeq Annotation chipseq

updated 15.5 years ago • Julie Zhu

What was the very first paper to describe "limma-trend"? By "limma-trend" I mean the one described in Law (2014), but I am not sure that was the first time. Thanks

limma

updated 10.2 years ago • Nik Tuzov

participating and presenting his/her work in this workshop may do it by sending a contribution. The papers should be written in English. There are three possibilities: 1- Long papers: A maximum length of 8 pages. They must consist...unpublished sound research results related to any of the topics of the conference. 2- Short papers: A maximum length of 4 pages. They can be project report, a summa…

updated 17.0 years ago • Nora Muda

div class="preformatted">Dear Colleague, We cordially invite you to submit a paper or invited session proposal to the upcoming 6th International Conference on Natural Computation (ICNC'10) and the...Island, and Penglai Pavilion Scenic Area. Seafood and fruits are plentiful in Yantai. Selected best papers will appear in SCI-indexed journal(s). All papers in conference proceedings will be inde…

updated 16.1 years ago • ICNC'10-FSKD'10

__FIRST CALL FOR PAPERS __ __CIBB 2015__ __12th International Meeting on Computational Intelligence Methods for Bioinformatics and...CNR Napoli The scientific programs of CIBB 2015 will include Keynote Speakers, contributed papers, tutorial and special sessions. The contributed papers will be presented in plenary oral sessions, special sessions...or poster sessions. __Publications_…

conference bioinformatics News

updated 10.8 years ago • rancoita.paola

<div class="preformatted">Hi, There is a new paper out at BMC bioinformatics that seems to justify the use of filtering before differential expression analysis is performed...div class="preformatted">Hi, There is a new paper out at BMC bioinformatics that seems to justify the use of filtering before differential expression analysis is...filter out the control genes before testing. I w…

Cancer Cancer

updated 16.9 years ago • Daniel Brewer

__ __<http://www.journals.elsevier.com/international-journal-of-approximate-reasoning/call-for-papers/special-issue-on-statistical-and-computational-methods-for-g/>   __Background and Scope:__ In the last decade, the...be also considered, as data have very high dimension and computational resources are limited.   Papers are sought on theoretical and practical…

news call News

updated 10.3 years ago • rancoita.paola

<div class="preformatted">(We are pleased to announce Keynote Speakers: Bir Bhanu, IEEE Fellow; Lixia Zhang, IEEE & ACM Fellow) (Due to many requests, the submission deadline is now extended to October 21, 2008) 2009 World Congress on Computer Science and Information Engineering (CSIE 2009) March 31 - April 2, 2009 Los Angeles/Anaheim, USA http://world-research-institutes.org/con…

updated 17.2 years ago • Linda Jones

all coming from the _limma_ package. For now I'm focusing on the ROAST procedure and reading the paper by Wu et al. (_ROAST: rotation gene set tests for complex microarray experiments_, 2010) I've learned how the gene set statistics...are defined (theoretically). For having some doubt about what was intended (in section 3.3 of the paper) for "weighted mean" (were the weights considered only in t…

limma roast statistics source code gene set testing

updated 7.3 years ago • Andrea Carenzo

Sequence Analysis & Alignment * SNPs and Haplotyping * System Biology and Modelling *Paper Submission Details:* * Authors are invited to submit original research contributions or experience reports in English...The submitted manuscript should closely reflect the final paper as it will appear in the proceedings of BIRD'08. * Papers should not exceed 15 pages i…

Genetics Pathways Cancer microRNA Genetics Pathways Cancer microRNA

updated 18.0 years ago • Prof. Roland Wagner

Dear Experts, I wonder if somebody contributed to or met biological! paper, where NGS and following bioinformatics are just one of the many methods used, and thus bioinformatics part is described

deseq2 edgeR

updated 8.3 years ago • Vladimir Krasikov

seq replicates, to observe test variation in repeated multiple test. Can anyone tell me any related papers, journal review to explain the topic that I raised? I also prefer to look at any existing Bioconductor packages that

bioinformatics paper multiple treatments biologicalreplicates

updated 9.4 years ago • Jurat Shahidin

I’m trying to recreate the results from this Alzheimer’s paper for further analysis (https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0355-3) Specifically...is the microarray expression data, called alzheimers ![Alzheimer's expression data][2] ``` #The paper divided up patients into 'normal', 'low', and 'high' alzheimers (supplementary table 2 of paper) and I am dividing…

limma edger linear regression microarray differential gene expression

updated 6.8 years ago • ravelarvargas

is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers: BCBGC-10, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and...guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for…

updated 15.8 years ago • John Edward

is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers: BCBGC-10, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and...guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for…

updated 15.6 years ago • John Edward

The submission deadline for this collection is May 31st. This is a firm deadline to ensure papers are published before BioC starts.  Articles will be published as and when they are ready, and we expect all contributions

publication workflows benchmark teaching News

updated 9.7 years ago • Wolfgang Huber

the vignette. I want to duplicate and RNASeq values and plots of an RNAseq exmaple in the quantro paper, before I apply quantro to my own data. I applied quantro to Bottomly et al.'s dataset (PMID:21455293) downloaded from recount...steps (eliminating all zero genes and running the rlogTransformation) which were mentioned in the paper. I got different quantro statistics and plots than in the…

quantro RNASeq

updated 5.5 years ago • raf4

is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers: BCBGC-10, Orlando, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics...guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.or…

updated 15.8 years ago • John Edward

is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers (Deadline Extended): BCBGC-10, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology...guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.o…

updated 15.7 years ago • John Edward

0500 > Subject: Re: [BioC] Filtering before differential expression analysis of microarrays - New paper out > Hi Dan, > > Daniel Brewer wrote: >> >> Hi, >> >> There is a new paper out at BMC bioinformatics that seems...out the control genes before testing. I was wondering if anyone had any >> opinio…

Microarray GO limma Microarray GO limma

updated 16.9 years ago • Sherosha Raj

R 4.1.0) curl 4.3.1 2021-04-30 [1] CRAN (R 4.1.0) data.table 1.14.0 2021-02-21 [1] CRAN (R 4.1.0) DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.0) dbplyr * 2.1.1 2021-04-06 [1...doParallel 1.0.16 2020-10-16 [1] CRAN (R 4.1.0) dotCall64 1.0-1 2021-02-11 [1] CRAN (R 4.1.0) dplyr …

spatialLIBD

updated 4.4 years ago • Dimitri

R 4.1.0) curl 4.3.1 2021-04-30 [1] CRAN (R 4.1.0) data.table 1.14.0 2021-02-21 [1] CRAN (R 4.1.0) DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.0) dbplyr 2.1.1 2021-04-06 [1...CRAN (R 4.1.0) DelayedArray 0.18.0 2021-05-19 [1] Bioconductor desc 1.3.0 2021-03-05 [1] CRAN (R 4.1.0)…

FunctionalAnnotation

updated 4.5 years ago • Catherine

broom 0.7.10 2021-10-31 [2] RSPM (R 4.1.0) cachem 1.0.6 2021-08-19 [2] RSPM (R 4.1.0) callr 3.7.0 2021-04-20 [2] RSPM (R 4.1.0) car 3.0-12 2021-11-06 [1] RSPM (R 4.1.0...1.14.3 2021-08-26 [1] Bioconductor deldir 1.0-6 2021-10-23 [2] RSPM (R 4.1.0) desc 1.4.0 …

BiocParallel muscat single-cell

updated 3.7 years ago • tangming2005

gt;=2 pages) due Sept 18, 2009  Acceptance notification Jan 15, 2010   Full paper submission For more information, please visit http://www.camda2009.org Sincerely, CAMDA2009 organizers [[alternative

Sequencing Sequencing

updated 16.3 years ago • Pan Du

to find that neither method has a cited reference despite being included in both the main limma paper and both edgeR and limma user guides. DEXSeq in comparison has a separate reference in addition to DESeq/DESeq2.&nbsp

edgeR limma diffSplice DEXSeq

updated 9.3 years ago • maltethodberg

12.2 2020-07-07 [1] > callr 3.7.0 2021-04-20 [1] circlize > * 0.4.13 2021-06-09 [1] cli 3.0.0 2021-06-30 [1] clisymbols 1.2.0 2017-05-21 [1] > clue 0.3-59 2021-04-16 [1] cluster...gt; later 1.2.0 2021-04-23 [1] lifecycle > …

anno_block ComplexHeatmap left_annotation right_annotation

updated 4.4 years ago • glich

3 MUT samples and 3 drug treated samples ``` WT1 - 12/14/2022 WT2 - 12/14/2022 WT3 - 11/03/2021 MUT1 - 11/03/2021 MUT2 - 11/03/2021 MUT3 - 11/03/2021 DRUG1 - 11/03/2021 DRUG2 - 12/03/2021 DRUG3 - 11/03/2021 ``` How can I make my sample info

DESeq2

updated 3.3 years ago • gv

easily  adaptable by other analysts to new data. The workflow may reproduce a previously published paper. * adhere to high standards of reproducibility and documentation for both data and code.  Implementation can be as a workflow

workflows publish News

updated 10.3 years ago • Levi Waldron

gt; Subject: Re: [BioC] Filtering before differential expression > analysis of microarrays - New paper out > > Hi Dan, > > > > Daniel Brewer wrote: > >> > >> Hi, > >> > >> There is a new paper out at BMC bioinformatics...the control genes before testing. I was wond…

Microarray GO limma Microarray GO limma

updated 16.9 years ago • Jenny Drnevich

I am trying to recreate the differential gene expression results from the following paper between Alzheimer’s and normal brain donors (https://genomemedicine.biomedcentral.com/articles/10.1186/s13073...I am trying to recreate the differential gene expression results from the following paper between Alzheimer’s and normal brain donors (https://genomemedicine.biomedcentral.com/articles/10.1186/s130…

limma microarray differential gene expression linear regression edger

updated 6.8 years ago • ravelarvargas

tracks and tables module, as reported following: STATUS STARTED Exporting sites 2021-03-07 15:36:10 2.6 STATUS STARTED Creating Track Hub -- bigBed 2021-03-07 15:36:10 2.6 WARNING Skipped conversion bed -> bigBed...for region type sites; could not find the tool bedToBigBed 2021-03-07 15:36:10 2.6 STATUS …

RnBeads

updated 4.8 years ago • Federica

3.3.6.9000 2022-07-21 [1] Github (tidyverse/ggplot2@a979ffd) ggplotify 0.1.0 2021-09-02 [1] CRAN (R 4.2.0) ggraph 2.0.5 2021-02-23 [1] CRAN (R 4.2.0) ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.2.0) ggridges 0.5.3 2021-01-08...2021-05-03 [1] CRAN (R 4.2.1) labeling 0.4.2 2020-10-20 [1] …

clusterProfiler

updated 3.4 years ago • Y.K