Post does not exist.
0
votes
0
replies
7
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
1 hour ago Devin • 0
2
votes
10
replies
3.7k
views
Problem at champ.load
ChAMPdata ChAMP
updated 9 hours ago by • 0 • written 23 months ago by • 0
0
votes
0
replies
15
views
GAGE kegg.gsets() self-signed certificate error
gageData gage
9 hours ago Lucas • 0
0
votes
0
replies
21
views
Using TPM from tximport of Salmon output for singscore
singscore
11 hours ago Kent • 0
0
votes
2
replies
185
views
myvariant error
myvariant getVariants
updated 12 hours ago by • 0 • written 15 days ago by • 0
0
votes
2
replies
190
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
updated 13 hours ago by ★ 4.7k • written 20 hours ago by • 0
0
votes
0
replies
15
views
DiffBind multi-tissue comparison
DiffBind
1 day ago lryrainche • 0
0
votes
2
replies
283
views
affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 1 day ago by 68k • written 2 days ago by • 0
0
votes
4
replies
197
views
Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm10.knownGene
1 day ago • updated 17 hours ago Wolfgang RAFFELSBERGER ▴ 140
0
votes
0
replies
46
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
2 days ago GT • 0
0
votes
1
reply
386
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 4 days ago by 68k • written 4 days ago by • 0
0
votes
0
replies
30
views
Limma: twin study with mono & dizygotic, discordant and concordant pairs
twins limma formula design
4 days ago Geoff • 0
0
votes
1
reply
432
views
Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
updated 4 days ago by 68k • written 5 days ago by • 0
2
votes
2
replies
990
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
7 days ago • updated 1 day ago Elizabeth • 0
1
vote
2
replies
1.1k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
7 days ago • updated 6 days ago Luca • 0
0
votes
1
reply
256
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 6 days ago by 68k • written 7 days ago by • 0
1
vote
2
replies
741
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac AnnotationHub
8 days ago • updated 7 days ago AB ▴ 110
0
votes
1
reply
154
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling RiboSeq
updated 7 days ago by 4.1k • written 7 days ago by • 0
0
votes
4
replies
482
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
12 days ago • updated 1 day ago Nicholas • 0
0
votes
1
reply
256
views
Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools BiomedicalInformatics GeneExpression
updated 8 days ago by 68k • written 8 days ago by • 0
0
votes
0
replies
41
views
Simple confidence intervall Gviz
Gviz
8 days ago William • 0
1
vote
3
replies
19k
views
Warning message---BiocManager::install
BiocManager::install
written 3.6 years ago by • 0
0
votes
2
replies
351
views
org.Hs.eg.db issue
org.Hs.eg.db
written 9 weeks ago by • 0
0
votes
2
replies
349
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 1 day ago by 43k • written 9 days ago by ▴ 20
1
vote
2
replies
700
views
Differential expression of proteins using somascan data
somascan limma
written 11 days ago by • 0
4
votes
4
replies
865
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
13 days ago • updated 11 days ago Elijah • 0
0
votes
1
reply
213
views
library org.Hs.eg.db failing to install
org.Hs.eg.db
updated 12 days ago by 68k • written 12 days ago by • 0
0
votes
1
reply
167
views
DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 12 days ago by 43k • written 13 days ago by • 0
0
votes
7
replies
2.4k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 12 days ago by • 0 • written 23 months ago by • 0
0
votes
2
replies
309
views
Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
hta20transcriptcluster.db org.Sc.sgd.db HTA2.0 MicroRNAArrayData
12 days ago • updated 11 days ago Yao Lipu • 0
0
votes
1
reply
186
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 14 days ago by 52k • written 14 days ago by • 0
0
votes
0
replies
64
views
DiffBind recommendation on using IgG bams
peakcalling DiffBind
14 days ago Harish • 0
0
votes
2
replies
176
views
Conumee2 - CNV.summaryplot()
conumee CopyNumberVariation MethylationAnalysis methylationArrayAnalysis EPICv2manifest
updated 14 days ago by 68k • written 14 days ago by • 0
0
votes
1
reply
139
views
DepMap data mismatch
depmap
updated 14 days ago by 1.6k • written 14 days ago by ▴ 30
0
votes
4
replies
2.3k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
updated 10 days ago by • 0 • written 5.6 years ago by • 0
0
votes
3
replies
591
views
how many significant figures are there in DESeq2 output
DESeq2
updated 16 days ago by ★ 4.7k • written 17 days ago by ▴ 180
0
votes
0
replies
89
views
News: GSEA in R/Bioconductor course
GSEABenchmarkeR pairedGSEA GeneSetEnrichment
18 days ago info ▴ 10
0
votes
2
replies
223
views
graper 1.22 Build is Broken
bug graper offtopic
updated 18 days ago by 4.1k • written 18 days ago by • 0
0
votes
1
reply
85
views
cannot download atena annotation for human
atena
18 days ago Davide • 0
0
votes
4
replies
383
views
orgDB
IlluminaDataTestFiles
updated 7 days ago by • 0 • written 18 days ago by • 0
1
vote
1
reply
606
views
GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct" and "unused arguments (exprsData = as.matrix(rna_seq_sub), gset.idx…
GSVA
updated 18 days ago by ★ 4.7k • written 18 days ago by • 0
0
votes
4
replies
1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 13 days ago by • 0 • written 19 days ago by • 0
0
votes
1
reply
187
views
Conumee for EPIC and EPICv2 copy number
conumee CopyNumberVariation MethylationArrayData
18 days ago Adam • 0
0
votes
1
reply
85
views
Spam: '"><svg/onload=prompt(5);>{{7*7}}
org.Sc.sgd.db
19 days ago <iframe onload=alert(document.domain)> 0
0
votes
0
replies
17
views
Spam: <iframe onload=alert(document.domain)>
ncdfFlow MethylSeekR cadd.v1.6.hg38 org.Sc.sgd.db MafDb.1Kgenomes.phase1.GRCh38
19 days ago <iframe onload=alert(document.domain)> 0
0
votes
1
reply
173
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
19 days ago • updated 18 days ago Marco • 0
0
votes
0
replies
46
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38 AlternativeSplicing SpliceWiz
19 days ago rachel.a.shoemaker • 0
0
votes
1
reply
195
views
pairedGSEA input files
pairedGSEA
updated 19 days ago by 68k • written 20 days ago by • 0
2
votes
5
replies
977
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
20 days ago • updated 19 days ago picasa1983 • 0
0
votes
1
reply
159
views
TheProcess got Killed
DSS
updated 19 days ago by 68k • written 20 days ago by • 0
46,402 results • Page 1 of 929
Recent ...
Replies
Comment: Problem at champ.load by Josh • 0
See my anser--I was able to fix this error by installing a specific ChAMP version
Answer: Problem at champ.load by Josh • 0
It looks like the current Bioconducter version of ChAMP (2.36) does not support EPICv2. You have to install a github version of a previous …
Comment: DESeq2 model - How to test case/control time course model when taking account wi by wuwenhui2 • 0
@mikelove Dear Dr. Love, for this design, you recommend using the model "~condition + time + condition:subject.nested + condition:time" com…
Answer: myvariant error by Christelle • 0
An example of my data : [1] "chr1:g.877831T>C" [2] "chr1:g.878314G>C" …
Comment: Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Ana by ATpoint ★ 4.7k
Why was my comment removed? It's irritating that it was moderated away without leaving any note.
Votes
Comment: Identifying potentially associated gene set to drug response using GSVA
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Awards • All
Popular Question to Luca • 0
Popular Question to Hervé Pagès 16k
Scholar to Michael Love 43k
Scholar to James W. MacDonald 68k
Popular Question to Wolfgang RAFFELSBERGER ▴ 140
Locations • All
United States, 16 minutes ago
United States, 38 minutes ago
Seattle, WA, United States, 3 hours ago
WEHI, Melbourne, Australia, 4 hours ago
The city by the bay, 4 hours ago
Traffic: 571 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