3
votes
2
replies
1.0k
views
Store Matrix in DataFrame Cell
S4Vectors
10 weeks ago • updated 9 weeks ago Dario Strbenac ★ 1.6k
0
votes
5
replies
965
views
For some reason I can't update BiocManager to 3.20
Bioconductor
updated 9 weeks ago by 4.1k • written 9 weeks ago by • 0
0
votes
0
replies
6
views
Spam: Link Slot Deposit Pulsa IM3 5000 RIBU : Maxwinbet77 Situs Gacor Online 24 Jam
netresponse hgu219.db MantelCorr IlluminaDataTestFiles
9 weeks ago Abu 0
0
votes
0
replies
6
views
Spam: Situs Slot Deposit ShopeePay 5 Ribu | Maxwinbet77 Link Aman & Terpercaya 2025
PhenoGeneRanker BSgenome.Osativa.MSU.MSU7 mouse.db0 SIM
9 weeks ago Abu 0
0
votes
0
replies
8
views
Spam: SLOT DEPOSIT TELKOMSEL 5 RIBU | Maxwinbet77 Link Gacor di Jamin Menguntungkan 2025!
Qtlizer ropls TransOmicsData MethylSeekR
9 weeks ago Abu 0
0
votes
0
replies
10
views
Spam: Maxwinbet77 Viral Slot Deposit Pulsa Tri 5 Ribu Gampang Menang Seru & Menguntungkan !!
proDA org.Sc.sgd.db TVTB
9 weeks ago Abu 0
0
votes
0
replies
10
views
Spam: Maxwinbet77 | Popularitas Slot Deposit Ovo 5000 Naik Meningkat & Menguntungkan
JobPosting customCMPdb TransOmicsData
9 weeks ago Abu 0
0
votes
0
replies
12
views
Spam: SLOT DANA 5K >> Situs Slot Deposit Dana 5000 Maxwinbet77 Tanpa Potongan Dinamis & Elegan
GOTHiC BubbleTree PANR
9 weeks ago Abu 0
0
votes
1
reply
260
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
10 weeks ago Jessica • 0
0
votes
0
replies
125
views
News: GBCC2025 Abstract Submissions & Registration Now Open!
Community Conference GBCC2025 Bioconductor
10 weeks ago Maria Doyle ▴ 100
0
votes
1
reply
186
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
0
votes
1
reply
466
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 10 weeks ago by ★ 4.8k • written 11 weeks ago by • 0
0
votes
1
reply
212
views
Error: lexical error: invalid char in json text (alevin-seurat)
tximpo tximportData alevinQC
updated 10 weeks ago by ★ 4.8k • written 10 weeks ago by • 0
0
votes
0
replies
94
views
Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq cumulativesumscaling
updated 10 weeks ago by 68k • written 10 weeks ago by • 0
0
votes
0
replies
231
views
Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf minfiDataEPIC MethylationArrayData MethylationArray EPICv2manifest
10 weeks ago charlie.wright • 0
0
votes
3
replies
567
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 10 weeks ago by • 0 • written 10 weeks ago by • 0
0
votes
4
replies
499
views
Web accessibility of Bioconductor.org
website Website
updated 10 weeks ago by 21k • written 10 weeks ago by • 0
1
vote
2
replies
815
views
Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = IntersectionNotEmpty)
GenomicAlignments summarizeOverlaps( Smart-seq2 proteinvariantcounting
10 weeks ago SofieK • 0
0
votes
2
replies
341
views
Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
11 weeks ago • updated 10 weeks ago a.alkema • 0
0
votes
2
replies
421
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 10 weeks ago by • 0 • written 11 weeks ago by • 0
0
votes
3
replies
485
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 8 weeks ago by • 0 • written 11 weeks ago by • 0
0
votes
3
replies
487
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 11 weeks ago by • 0 • written 12 weeks ago by ▴ 10
5
votes
5
replies
1.2k
views
Unused arguments error without used arguments in GSVA?
GSVA
updated 28 days ago by • 0 • written 11 weeks ago by • 0
0
votes
1
reply
1.1k
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 11 weeks ago by 43k • written 4.0 years ago by • 0
1
vote
1
reply
1.7k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 11 weeks ago by 43k • written 4.5 years ago by • 0
4
votes
3
replies
418
views
plyranges: find exact GRanges match keeping metadata columns
plyranges
updated 10 weeks ago by 43k • written 11 weeks ago by • 0
0
votes
0
replies
123
views
News: Mass Spectrometry and Proteomics with R/Bioconductor course
cadd.v1.6.hg38
11 weeks ago info ▴ 10
0
votes
1
reply
201
views
Restricting differential binding analysis to only TSS-proximal regions
ChIP csaw
updated 11 weeks ago by ★ 28k • written 11 weeks ago by • 0
0
votes
0
replies
123
views
Batch Correction while implementing QSEA package
qsea MEDIPS MEDIPSData DNAMethylation
11 weeks ago User3088 • 0
0
votes
0
replies
113
views
News: Announcing the GBCC2025 Logo Design Winner!
Community Conference GBCC2025 Bioconductor
11 weeks ago Maria Doyle ▴ 100
0
votes
1
reply
163
views
building samplesheet and plot profile
DiffBind
11 weeks ago yf • 0
0
votes
0
replies
87
views
DBT JRF & PhD Scholar
BiologicalQuestion OmicsMLRepoR
11 weeks ago Manisha • 0
0
votes
1
reply
233
views
I am having issues with bowtie2_build
genomes bowtiew Index
updated 11 weeks ago by 68k • written 12 weeks ago by • 0
0
votes
1
reply
278
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 11 weeks ago by 43k • written 12 weeks ago by • 0
0
votes
0
replies
136
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
12 weeks ago cftattersfield • 0
1
vote
0
replies
291
views
News: Bioconductor Course, Kenya 2025: Applications Open!
Events Community Training Africa Bioconductor
12 weeks ago Maria Doyle ▴ 100
0
votes
2
replies
591
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
12 weeks ago • updated 9 weeks ago ingrid.h • 0
2
votes
2
replies
500
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by • 0
9
votes
3
replies
2.2k
views
Job: Postdoc/RA position: Software Engineer For R and High-Performance Computing
JobPosting CuratedAtlasQueryR tidySpatialExperiment tidyomics tidySingleCellExperiment
written 10 months ago by ▴ 40
0
votes
4
replies
1.0k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
12 weeks ago Quang NN ▴ 10
1
vote
3
replies
776
views
Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 12 weeks ago by • 0 • written 12 weeks ago by • 0
4
votes
9
replies
2.3k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 12 weeks ago by ★ 3.4k • written 4 months ago by ▴ 20
0
votes
1
reply
257
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 12 weeks ago by ★ 4.8k • written 3 months ago by • 0
0
votes
2
replies
270
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
3 months ago • updated 12 weeks ago Vinesh • 0
0
votes
1
reply
164
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 12 weeks ago by ★ 4.8k • written 12 weeks ago by • 0
0
votes
1
reply
217
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 12 weeks ago by 68k • written 3 months ago by • 0
0
votes
2
replies
784
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
3 months ago • updated 12 weeks ago Blandine • 0
0
votes
5
replies
417
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 3 months ago by • 0
0
votes
1
reply
194
views
affymetrix
genomes Annotation
updated 3 months ago by 68k • written 3 months ago by • 0
0
votes
1
reply
912
views
Problems with GSEA
GSEABase
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
46,462 results • Page 4 of 930
Recent ...
Replies
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much for the vis suggestion!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - I appreciate the mathematical explanation and link to Dr. Phipson's thesis!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - this is very clear!
Answer: How do I set up my DESeq analysis when I know a few vehicle control samples prov by Michael Love 43k
I think it will capture it automatically. E.g. if you use the method that focuses on genes lowly or not affected by the treatment, then the…
Votes
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
Awards • All
Popular Question to Szabolcs • 0
Popular Question to Gordon Smyth 52k
Popular Question to shepherl 4.1k
Popular Question to Mengjun • 0
Popular Question to James W. MacDonald 68k
Locations • All
Japan, 41 minutes ago
United States, 1 hour ago
United States, 1 hour ago
The city by the bay, 2 hours ago
Canada, 2 hours ago
Traffic: 695 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6