0
votes
1
reply
452
views
Rain error: invalid annotation of time points
rain
updated 2 hours ago by • 0 • written 10 months ago by • 0
2
votes
4
replies
306
views
EdgeR Biological CVs
edgeR
updated 3 hours ago by 52k • written 3 days ago by • 0
0
votes
1
reply
76
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
updated 6 hours ago by ★ 4.1k • written 22 hours ago by • 0
0
votes
0
replies
18
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
10 hours ago Anki • 0
1
vote
4
replies
2.8k
views
CUT&Tag differential peak analysis using Diffbind, with pre-calculated normalization factor.
DiffBind
updated 14 hours ago by • 0 • written 3.8 years ago by • 0
0
votes
4
replies
317
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
3 days ago • updated 1 day ago Quang NN ▴ 10
0
votes
4
replies
2.2k
views
How can I generate a heatmap and clustering of differentially expressed genes in a RNA-seq data?
Heat Map. FPKM. p_value. FDR
updated 1 day ago by • 0 • written 4.7 years ago by • 0
0
votes
4
replies
152
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
1 day ago georgeyu703 • 0
0
votes
2
replies
1.1k
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.9 years ago by • 0
0
votes
1
reply
83
views
affymetrix
genomes Annotation
updated 1 day ago by 67k • written 2 days ago by • 0
0
votes
1
reply
101
views
Problems with GSEA
GSEABase
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
0
votes
0
replies
30
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
2 days ago Vinesh • 0
0
votes
1
reply
123
views
Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19)
Rbowtie
5 days ago • updated 2 days ago ja.garcia • 0
0
votes
3
replies
303
views
Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA RNASeqPower DEGseq
written 9 weeks ago by • 0
0
votes
1
reply
755
views
News: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and Galaxy!
Conference Bioconductor Community
written 4 months ago by ▴ 90
1
vote
2
replies
413
views
contrast matrix design for a continuous variable
limma
7 weeks ago • updated 2 days ago dtzhu337 • 0
1
vote
1
reply
121
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 2 days ago by ▴ 750 • written 6 days ago by • 0
0
votes
11
replies
610
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 3 days ago by • 0 • written 7 days ago by • 0
2
votes
9
replies
729
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
15 days ago • updated 3 days ago Quang NN ▴ 10
0
votes
0
replies
40
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
3 days ago Reuben • 0
0
votes
1
reply
212
views
Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond fish
updated 4 days ago by 43k • written 6 days ago by • 0
0
votes
0
replies
27
views
Problem with PCAtool as dependencie
COTAN PCAtools
4 days ago Silvia • 0
1
vote
2
replies
211
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData signatureSearchData StatisticalMethod
written 8 weeks ago by • 0
0
votes
2
replies
46k
views
SingleR Label.Ont
SingleR
written 16 months ago by • 0
3
votes
5
replies
4.8k
views
plotMDS in edgeR
edger rnaseq
written 9.3 years ago by ▴ 30
3
votes
6
replies
1.4k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 10 months ago by • 0
0
votes
0
replies
33
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
6 days ago xiaofeiwang18266 ▴ 50
0
votes
1
reply
162
views
Job: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal Patterning
JobPosting
updated 6 days ago by • 0 • written 5 weeks ago by ★ 2.0k
2
votes
5
replies
697
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 6 days ago by 67k • written 6 days ago by ▴ 10
0
votes
1
reply
96
views
XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 6 days ago by 67k • written 8 days ago by • 0
0
votes
2
replies
173
views
Error using useMart or useEnsembl
biomaRt
updated 6 days ago by 67k • written 7 days ago by • 0
2
votes
1
reply
456
views
Error in download.file for TCGAutils::symbolsToRanges
TCGAutils
updated 7 days ago by 67k • written 7 days ago by ▴ 50
0
votes
2
replies
225
views
DESeq2 Heatmap
heatmaps
updated 7 days ago by ★ 1.4k • written 8 days ago by • 0
0
votes
4
replies
259
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 7 days ago by 67k • written 8 days ago by • 0
0
votes
1
reply
95
views
Unknown gene transcripts after annotatr
annotatr
updated 7 days ago by 67k • written 8 days ago by • 0
2
votes
5
replies
291
views
Differential variability modelling with vst() expression
limma DESeq2
written 13 days ago by • 0
0
votes
1
reply
88
views
Improve performance of qusage aggregateGeneSet
qusage
updated 8 days ago by 67k • written 8 days ago by • 0
0
votes
0
replies
71
views
gsameth GSA: probe annotation to multiple genes
missMethyl gsameth
9 days ago nurkenber • 0
0
votes
1
reply
141
views
org.Hs.eg.db issue
org.Hs.eg.db
updated 9 days ago by 4.1k • written 11 days ago by • 0
0
votes
0
replies
77
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
9 days ago GJ • 0
0
votes
1
reply
78
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 9 days ago by 67k • written 10 days ago by ▴ 20
0
votes
0
replies
58
views
News: Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
11 days ago info ▴ 10
1
vote
4
replies
1.8k
views
MBDseq analysis using qsea package
qsea MBDseq
updated 11 days ago by ▴ 20 • written 5.4 years ago by • 0
0
votes
2
replies
355
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
14 days ago • updated 12 days ago sindhuri • 0
0
votes
2
replies
357
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 12 days ago by ▴ 840
0
votes
2
replies
224
views
iam not able to do retrive data using GEOquery R package
HELP
updated 12 days ago by 67k • written 13 days ago by • 0
2
votes
8
replies
526
views
Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) returning drastically different numbers of transcripts
AnnotationDbi EnsDb.Mmusculus.v79 biomaRt org.Mm.eg.db
updated 12 days ago by 67k • written 14 days ago by • 0
0
votes
2
replies
130
views
Installation error for Rsamtools.
Rsamtools
updated 13 days ago by ★ 4.6k • written 13 days ago by • 0
0
votes
0
replies
59
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
14 days ago Maggie • 0
1
vote
3
replies
888
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 14 days ago by 67k • written 16 months ago by • 0
1,437 results • Page 1 of 29
Recent ...
Replies
Comment: Rain error: invalid annotation of time points by Dominik • 0
Hi, I kept running into the same issue until I double checked their help and understood, that columns and rows have to be designed in anoth…
Answer: How to generate circular cnetplot and color nodes and edges in the same plot ? by Guido Hooiveld ★ 4.1k
Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mec25 • 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10
Thank you so much for taking time to provide this clarification!
Comment: How can I generate a heatmap and clustering of differentially expressed genes in by Renuka • 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Awards • All
Popular Question to shepherl 4.1k
Popular Question to Martin Morgan 25k
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to Joseph Fass ▴ 70
Popular Question to Peter Hickey ▴ 750
Locations • All
France, 4 minutes ago
China, 22 minutes ago
Spain, 44 minutes ago
United States, 45 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Traffic: 1006 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