0
votes
2
replies
248
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 weeks ago by 42k • written 6 weeks ago by ▴ 30
0
votes
1
reply
191
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
votes
2
replies
267
views
Regressing out batch effects
DESeq2
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
5
votes
6
replies
462
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
0
votes
1
reply
164
views
BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
1
vote
6
replies
526
views
GSVA on separate healthy and disease datasets
GSVA
updated 5 weeks ago by 65k • written 5 weeks ago by ▴ 60
0
votes
0
replies
132
views
ggtree tip label position (depth)
ggtree
5 weeks ago Roope • 0
2
votes
6
replies
467
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
5 weeks ago Chris ▴ 10
0
votes
1
reply
192
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 5 weeks ago by 65k • written 6 weeks ago by • 0
0
votes
0
replies
175
views
Job: PhD-position in bioinformatics / computational biology
Mergeomics Epigenome Evolution NGS Aging
5 weeks ago arne.sahm • 0
0
votes
0
replies
114
views
News: Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry conference
5 weeks ago Wolfgang Huber ★ 13k
1
vote
10
replies
480
views
Obtaining pheno data from CEL files
GEO affy
6 weeks ago • updated 5 weeks ago Kurtis • 0
0
votes
1
reply
187
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
1
vote
3
replies
283
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
1
vote
2
replies
259
views
MethylKit read issue
methylKit
updated 6 weeks ago by 65k • written 7 weeks ago by • 0
1
vote
2
replies
3.2k
views
Extract genes from ggvenn?
ggvenn
updated 6 weeks ago by ▴ 10 • written 2.1 years ago by • 0
0
votes
4
replies
332
views
Help with design.matrix
limma
6 weeks ago andrea.rodriguez-martinez13 • 0
0
votes
0
replies
164
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
6 weeks ago andromeda • 0
0
votes
2
replies
183
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
2
votes
2
replies
219
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 6 weeks ago by ★ 4.1k • written 6 weeks ago by ★ 1.5k
0
votes
1
reply
146
views
Granges regionCounts not returning the expected number of entries
methylKit
6 weeks ago Modoc Kesner ▴ 10
0
votes
0
replies
117
views
flowDensity on a flowset
flowDensity
6 weeks ago fredrikwallberg • 0
1
vote
1
reply
190
views
DESeq2 - Missing values in count matrix
DESeq2
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
7
votes
39
replies
5.8k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 2 days ago by • 0 • written 5.5 years ago by ★ 4.0k
1
vote
2
replies
375
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
6 weeks ago • updated 16 days ago Kim • 0
0
votes
0
replies
106
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
6 weeks ago Macsue • 0
1
vote
4
replies
463
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 6 weeks ago by • 0 • written 5.3 years ago by • 0
0
votes
2
replies
807
views
error in install immunedeconv
Install
updated 6 weeks ago by • 0 • written 14 months ago by • 0
1
vote
6
replies
459
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
votes
2
replies
207
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 weeks ago Gimena • 0
0
votes
2
replies
199
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
2
votes
6
replies
1.6k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 6 weeks ago by ▴ 180 • written 5 months ago by ▴ 10
0
votes
6
replies
371
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 5 weeks ago by ▴ 180 • written 6 weeks ago by • 0
1
vote
1
reply
173
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
6 weeks ago Layal • 0
0
votes
2
replies
244
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
7 weeks ago • updated 6 weeks ago w.cookson • 0
0
votes
2
replies
187
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
6 weeks ago michelafrancesconi8 • 0
0
votes
1
reply
168
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
votes
4
replies
287
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
votes
4
replies
449
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
6 weeks ago Lucy ▴ 60
0
votes
1
reply
128
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
votes
2
replies
200
views
How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
7 weeks ago • updated 6 weeks ago Seongsu • 0
0
votes
2
replies
194
views
Gene Ontology doubt
microbiomeExplorer
7 weeks ago • updated 6 weeks ago Bhawna • 0
0
votes
1
reply
194
views
Convert transcriptomic bam to genomic bam?
ensembldb transcriptome genome coordinateconversion
updated 6 weeks ago by 42k • written 7 weeks ago by ▴ 10
0
votes
1
reply
176
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 6 weeks ago by 65k • written 7 weeks ago by • 0
0
votes
2
replies
316
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR CopyhelpeR
7 weeks ago • updated 6 weeks ago fer_talavera • 0
0
votes
2
replies
285
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
7 weeks ago • updated 4 weeks ago isaac.vock • 0
0
votes
7
replies
443
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
7 weeks ago • updated 6 weeks ago needNGS • 0
15
votes
23
replies
2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 19 days ago Chris ▴ 10
3
votes
5
replies
414
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
45,674 results • Page 5 of 914
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by jane • 0
Your material was totally correct, therefore I was able to learn what I needed to know. I'd want to convey my heartfelt gratitude for shari…
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Awards • All
Popular Question to Hussain • 0
Popular Question to euge.eugenio ▴ 20
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Locations • All
Spain, 4 minutes ago
The city by the bay, 38 minutes ago
Pakistan, 44 minutes ago
Greece, 50 minutes ago
South Africa, 52 minutes ago
Traffic: 597 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