2
votes
2
replies
415
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
9 days ago • updated 5 days ago Matthew Thornton ▴ 360
0
votes
1
reply
188
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
0
votes
0
replies
88
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer ShinyApps
11 days ago neilzhao ▴ 30
0
votes
1
reply
116
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 12 days ago by ★ 4.1k • written 12 days ago by • 0
1
vote
2
replies
291
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
12 days ago • updated 11 days ago Dylan.Sheerin • 0
2
votes
7
replies
430
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
13 days ago • updated 10 days ago sajadahmad41454 • 0
0
votes
0
replies
79
views
Treeio as.treedata function seq lenght error
treeio
13 days ago nromerov • 0
2
votes
2
replies
287
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
14 days ago • updated 8 days ago zzrammal • 0
3
votes
10
replies
494
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 11 days ago by 66k • written 14 days ago by • 0
0
votes
1
reply
122
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 14 days ago by 3.9k • written 14 days ago by • 0
2
votes
1
reply
191
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 14 days ago by 66k • written 14 days ago by • 0
0
votes
0
replies
100
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
15 days ago • updated 14 days ago Dinesh • 0
3
votes
5
replies
307
views
Help with running egsea()
EGSEA
15 days ago • updated 13 days ago Chris ▴ 10
3
votes
1
reply
157
views
How to save the DEXSeq results
DEXSeq
updated 15 days ago by 42k • written 15 days ago by • 0
2
votes
1
reply
150
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 15 days ago by 42k • written 15 days ago by ▴ 70
0
votes
3
replies
238
views
Couldn't connect to server while using "pathways"
graphite
updated 15 days ago by 42k • written 15 days ago by • 0
4
votes
5
replies
344
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
15 days ago • updated 6 days ago Chris ▴ 10
7
votes
6
replies
646
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 16 days ago by • 0
2
votes
2
replies
240
views
fgsea significant result
fgsea
16 days ago Chris ▴ 10
1
vote
2
replies
410
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 17 days ago by 50k • written 18 days ago by • 0
2
votes
3
replies
288
views
package goseq seems to be not available on the latest version of R
goseq
updated 15 days ago by 50k • written 18 days ago by ▴ 20
2
votes
3
replies
264
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 16 days ago by ★ 4.1k • written 18 days ago by • 0
1
vote
1
reply
196
views
Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by 42k • written 18 days ago by ▴ 10
0
votes
0
replies
125
views
dba.plotProfile() plotting and interpretation
DiffBind
18 days ago Henry ▴ 10
0
votes
6
replies
309
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 17 days ago by ★ 1.4k • written 19 days ago by ▴ 130
4
votes
2
replies
643
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
19 days ago • updated 15 days ago gene_bioconductor ▴ 10
0
votes
1
reply
181
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 18 days ago by 50k • written 19 days ago by • 0
0
votes
1
reply
166
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 18 days ago by 50k • written 19 days ago by • 0
0
votes
0
replies
100
views
flowStats for CyTOF
flowStats
19 days ago tholmes • 0
0
votes
2
replies
175
views
DESeq2 v1.35.0
DESeq2
updated 19 days ago by 42k • written 19 days ago by • 0
0
votes
0
replies
97
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
19 days ago yvonneh • 0
0
votes
0
replies
89
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
19 days ago Ian D. ▴ 70
0
votes
1
reply
146
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 19 days ago by • 0
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago kcarey • 0
0
votes
3
replies
231
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 days ago by ★ 4.1k • written 19 days ago by • 0
1
vote
3
replies
310
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 13 days ago by ★ 4.1k • written 20 days ago by • 0
4
votes
0
replies
147
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
20 days ago shepherl 3.9k
0
votes
0
replies
142
views
Empty table plot using plotGseaTable()
fgsea
20 days ago • updated 18 days ago Chris ▴ 10
3
votes
4
replies
298
views
Store output of matchPWM()
biostrings Biostrings
20 days ago • updated 8 days ago mat149 ▴ 70
0
votes
4
replies
381
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 10 days ago by • 0 • written 20 days ago by ▴ 70
1
vote
2
replies
297
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
20 days ago • updated 19 days ago Yveto • 0
0
votes
3
replies
307
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
3
votes
4
replies
270
views
Help with error using camera() in limma
CAMERA limma
21 days ago Chris ▴ 10
1
vote
1
reply
161
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
0
votes
0
replies
96
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
21 days ago Maria Doyle ▴ 70
0
votes
1
reply
141
views
putting my own expression data in deseq2
DESeq2
updated 21 days ago by ★ 4.1k • written 21 days ago by • 0
0
votes
2
replies
173
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
21 days ago • updated 18 days ago Aurora • 0
0
votes
1
reply
128
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 21 days ago by 3.9k • written 21 days ago by • 0
0
votes
1
reply
268
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 21 days ago by 66k • written 21 days ago by • 0
0
votes
1
reply
141
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 21 days ago by 42k • written 22 days ago by • 0
1,000 results • Page 2 of 20
Recent ...
Replies
Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Awards • All
Scholar to Mike Smith ★ 6.5k
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to bas_work ▴ 30
Popular Question to landenshanie ▴ 40
Locations • All
United States, 7 minutes ago
United States, 10 minutes ago
United States, 17 minutes ago
Spain, 43 minutes ago
United States, 50 minutes ago
Traffic: 660 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