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News: Single Package Builder / New Package Submission
new package build machines infrastructure News
5.4 years ago shepherl 4.2k
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deseq2 DESeqDataSet size when saved
deseq2 infrastructure deseqdataset importing
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
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News: Bioconductor git transition BETA phase starts now.
git svn infrastructure bioconductor News
8.3 years ago nitesh.turaga ▴ 140
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The bioconductor.org main website will be down for a brief period for maintenance. Starting approximately 7:45 am EST. Should be back up around 8:00 …
infrastructure
8.8 years ago gregory.wargula ▴ 30
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Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 9.2 years ago by • 0 • written 15.5 years ago by ★ 1.6k
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News: BioCAsia, 4th November 2016, Brisbane, Australia
conference transcription epigenomics visualization infrastructure News
9.3 years ago Matthew Ritchie ▴ 1000
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News: BioCAsia, 8 Sept 2015, Tokyo
sequencing transcription epigenomics visualization infrastructure News
10.4 years ago • updated 10.2 years ago Matthew Ritchie ▴ 1000
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Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 11.6 years ago by ★ 1.3k • written 11.6 years ago by ▴ 680
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job: head of core facility bioinformatics (Mainz/Germany)
Epigenetics Infrastructure Epigenetics Infrastructure
11.8 years ago Holger Klein ▴ 20
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Bioinformatics Facility Director Position at UC Riverside
Proteomics Infrastructure Proteomics Infrastructure
12.1 years ago Thomas Girke ★ 1.7k
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1.4k
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Reopening of Computational Biologist position at Genentech
Infrastructure PROcess Infrastructure PROcess
12.2 years ago Michael Lawrence ★ 11k
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*Ranges paper published
Infrastructure IRanges GenomicFeatures GenomicRanges Infrastructure IRanges GenomicFeatures
updated 12.2 years ago by ★ 4.2k • written 12.2 years ago by ★ 11k
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DexSeq extracols option
RNASeq Microarray Genetics Annotation Normalization Infrastructure Cancer probe limma
updated 12.3 years ago by ★ 1.9k • written 12.3 years ago by ▴ 40
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convert IDs in a data frame?
GO Infrastructure Cancer GO Infrastructure Cancer
updated 12.3 years ago by ★ 7.2k • written 12.3 years ago by 16k
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Finding mismatches between reads and reference sequence
Infrastructure Cancer BSgenome BSgenome Infrastructure Cancer BSgenome BSgenome
updated 12.6 years ago by ▴ 30 • written 12.6 years ago by 16k
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Bioconductor Digest, Vol 121, Issue 29
miRNA Annotation Normalization Visualization Clustering Infrastructure Cancer BSgenome vsn
12.6 years ago Matthew Thornton ▴ 380
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2
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3.0k
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[R] Error in setMethod("combine"... was - Error when installing globaltest package
Infrastructure Cancer Biobase tkWidgets globaltest BiocInstaller BiocGenerics Cancer
updated 12.6 years ago by 25k • written 12.6 years ago by ▴ 40
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Job: Bioinformatician (postdoc, indefinite) Pirbright Institute
Infrastructure Infrastructure
12.6 years ago Jan T Kim ▴ 50
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assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray Annotation GO Network Regression Survival Infrastructure Escherichia coli ROC
12.6 years ago Julie Zhu ★ 4.3k
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GSEABase error parsing msigdb_v3.1.xml
GO Infrastructure hgu95av2 Biobase annotate graph Category AnnotationDbi BiocGenerics GO
updated 12.8 years ago by 25k • written 12.8 years ago by ▴ 80
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Open computational biologist position at Genentech
Infrastructure Infrastructure
12.8 years ago Michael Lawrence ★ 11k
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1.4k
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Bioinformatics Position Opening
Proteomics Infrastructure Proteomics Infrastructure
12.8 years ago Thomas Girke ★ 1.7k
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1.9k
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Bioinformatician Job at Pirbright Institute
Genetics Infrastructure Genetics Infrastructure
12.9 years ago Jan T Kim ▴ 50
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5
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1.5k
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pooling for parallel hierarchical operations
Infrastructure Infrastructure
updated 13.0 years ago by 25k • written 13.0 years ago by ★ 11k
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counting RNA-seq reads in R/BioC
GO Infrastructure Rsubread easyRNASeq GO Infrastructure Rsubread easyRNASeq
updated 13.1 years ago by ★ 6.8k • written 13.1 years ago by ▴ 880
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good news and bad news
Infrastructure Cancer IRanges GenomicRanges Infrastructure Cancer IRanges GenomicRanges
updated 13.2 years ago by ★ 13k • written 13.2 years ago by 16k
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Bioinformatics Academic Coordinator Job Posting
Proteomics Infrastructure Proteomics Infrastructure
13.3 years ago Guest User ★ 13k
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2012 Bioconductor European Developers' Workshop - annoucement
Proteomics Infrastructure Proteomics Infrastructure
13.4 years ago Mark Robinson ▴ 880
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Open Position - Academic Coordinator for Bioinformatics
Proteomics Infrastructure Proteomics Infrastructure
13.6 years ago Thomas Girke ★ 1.7k
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2 more Job Announcements
Genetics Infrastructure Genetics Infrastructure
13.6 years ago Jenny Drnevich ★ 2.0k
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[Job] Bioinformatician-NGS (Vienna, Austria)
Sequencing Infrastructure Sequencing Infrastructure
13.9 years ago Ido M. Tamir ▴ 150
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"internal equal" overlap mode for GRangesList
Infrastructure Infrastructure
updated 14.0 years ago by ★ 1.6k • written 14.0 years ago by ★ 11k
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illuminaHumanv4 mappings
Infrastructure Cancer Homo sapiens probe AnnotationDbi ASSIGN Infrastructure Cancer probe
14.1 years ago Mark Cowley ▴ 910
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GGtools and GGBase installation problems
Infrastructure GUI Ruuid GGtools GGBase Infrastructure GUI Ruuid GGtools GGBase
updated 14.7 years ago by 6.7k • written 14.7 years ago by ▴ 460
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A code kata: evening-out *Ranges ends.
Infrastructure Cancer IRanges Infrastructure Cancer IRanges
15.2 years ago Steve Lianoglou ★ 13k
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NOTE: bioconductor.org system maintenance; planned downtime 12pm-1pm PDT Friday 9/18
Infrastructure Infrastructure
16.1 years ago Patrick Aboyoun ★ 1.6k
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Research positions available in neuroproteomics
Proteomics Infrastructure Proteomics Infrastructure
16.7 years ago Abhilash Venu ▴ 340
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GSEA to discover co-regulated genes
Transcription Annotation Pathways Infrastructure probe convert GSEABase Transcription
16.7 years ago Paul Geeleher ★ 1.3k
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1.1k
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Project Enquiry!
Infrastructure Infrastructure
17.2 years ago Kat ▴ 20
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Staff Position at EBI: Computational Scientist / Bioconductor
Infrastructure Infrastructure
17.2 years ago Wolfgang Huber ★ 13k
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1.7k
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GSEABase error in parsing msigdb_v2.5.xml
GO Infrastructure hgu95av2 Biobase Ruuid AnnotationDbi GO Infrastructure hgu95av2 Biobase
updated 17.5 years ago by 25k • written 17.5 years ago by ▴ 130
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Affymetrix Human Gene 1.0 ST Array
Infrastructure cdf probe affy Infrastructure cdf probe affy
17.5 years ago Hans-Ulrich Klein ▴ 330
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1.6k
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BioC 2.2 now available
SNP Microarray Genetics Annotation Preprocessing Bayesian Clustering Infrastructure Cancer
updated 17.5 years ago by ★ 1.6k • written 17.5 years ago by 25k
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To biomaRt users: Major downtime March 7th 4pm - March 8th 6pm
Infrastructure biomaRt Infrastructure biomaRt
17.7 years ago Steffen ▴ 500
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biocep project - R for the Web and the Virtual R Workbench
Infrastructure PROcess Infrastructure PROcess
18.0 years ago kchine@ebi.ac.uk ▴ 10
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question regarding lumiHumanV1SUMFUNC and lumiRatV1SUMFUNC in lumiHumanV1 and lumiRatV1, respectively
Annotation Infrastructure Cancer Annotation Infrastructure Cancer
18.2 years ago Seth Falcon ★ 7.4k
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2x2 factorial with dye effect, limma design
Microarray Infrastructure Microarray Infrastructure
18.8 years ago Gordon Smyth 53k
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1.6k
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BioC 1.9 is released!
BiocViews SNP Microarray Annotation Normalization Visualization Network Infrastructure SNP
19.1 years ago Seth Falcon ★ 7.4k
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1.4k
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Newbie 'rflowcyt' question; problem loading facscan256.fcs
Survival Infrastructure Cancer hexbin prada rfcdmin rflowcyt Survival Infrastructure
updated 19.4 years ago by ★ 7.4k • written 19.4 years ago by ▴ 80
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extracting interactions between members of the KEGG pathways
Pathways Infrastructure Cancer graph Pathways Infrastructure Cancer graph
updated 19.6 years ago by ★ 5.5k • written 19.6 years ago by ▴ 90
57 results • Page 1 of 2
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Replies
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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