0
votes
1
reply
715
views
Error in cnetplot
enrichplot clusterProfiler
updated 9 months ago by ★ 4.1k • written 10 months ago by • 0
0
votes
3
replies
892
views
getBM from biomaRt inconsistencies found with .gtf files across multiple species
.gtf biomaRt Ensembl
updated 9 months ago by ★ 6.6k • written 9 months ago by ▴ 20
2
votes
4
replies
1.0k
views
Explanation for ROAST results
CAMERA limma
written 9 months ago by • 0
1
vote
1
reply
478
views
Merging annotation with differential expression output
annotation RNASeqData
updated 9 months ago by 68k • written 9 months ago by • 0
0
votes
2
replies
676
views
Annotation package for Manduca sexta
annotation Manducasexta AnnotationData
9 months ago GA ▴ 10
0
votes
5
replies
1.0k
views
Bioconductor unable to update 'curl'
curl HELP
9 months ago kagodwi2 • 0
0
votes
1
reply
390
views
best way to grouping GSM belonging to different datasets (with different platforms) and compare differential gene expression
GEOquery
updated 9 months ago by 68k • written 9 months ago by • 0
1
vote
2
replies
1.4k
views
CpGs with genomic positions greater than the chromosome size in EPICv2?
EPICv2 EPICv2manifest
9 months ago Joshua Llano • 0
1
vote
4
replies
829
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
9 months ago Lennie • 0
4
votes
5
replies
1.8k
views
Using TPM from tximport of Salmon output for singscore
singscore
10 months ago • updated 9 months ago Kent • 0
5
votes
3
replies
1.3k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 10 months ago by 53k • written 10 months ago by ▴ 10
2
votes
10
replies
4.7k
views
Problem at champ.load
ChAMPdata ChAMP
updated 10 months ago by • 0 • written 2.7 years ago by • 0
0
votes
1
reply
522
views
GAGE kegg.gsets() self-signed certificate error
gageData gage
10 months ago • updated 9 months ago Lucas • 0
0
votes
2
replies
456
views
myvariant error
myvariant getVariants
updated 10 months ago by • 0 • written 10 months ago by • 0
0
votes
4
replies
1.4k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 10 months ago by • 0
0
votes
0
replies
271
views
DiffBind multi-tissue comparison
DiffBind
10 months ago lryrainche • 0
1
vote
2
replies
725
views
affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
0
replies
539
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
10 months ago GT • 0
1
vote
2
replies
1.2k
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
10 months ago • updated 7 months ago Erika • 0
0
votes
2
replies
883
views
Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
10 months ago DavideSant • 0
2
votes
2
replies
1.7k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
10 months ago Elizabeth • 0
1
vote
8
replies
2.8k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
10 months ago • updated 9 months ago Luca • 0
0
votes
1
reply
505
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 10 months ago by 68k • written 10 months ago by • 0
1
vote
3
replies
1.3k
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac AnnotationHub
written 10 months ago by ▴ 110
0
votes
1
reply
466
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling RiboSeq
updated 10 months ago by 4.3k • written 10 months ago by • 0
0
votes
4
replies
919
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
10 months ago Nicholas • 0
0
votes
1
reply
646
views
Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools BiomedicalInformatics GeneExpression
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
0
replies
314
views
Simple confidence intervall Gviz
Gviz
10 months ago William • 0
1
vote
3
replies
21k
views
Warning message---BiocManager::install
BiocManager::install
written 4.4 years ago by • 0
0
votes
2
replies
692
views
org.Hs.eg.db issue
org.Hs.eg.db
written 12 months ago by • 0
0
votes
2
replies
815
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 10 months ago by 43k • written 10 months ago by ▴ 20
1
vote
2
replies
1.1k
views
Differential expression of proteins using somascan data
somascan limma
written 10 months ago by • 0
0
votes
1
reply
734
views
library org.Hs.eg.db failing to install
org.Hs.eg.db
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
1
reply
489
views
DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
2
replies
627
views
Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
hta20transcriptcluster.db org.Sc.sgd.db HTA2.0 MicroRNAArrayData
10 months ago Yao Lipu • 0
0
votes
1
reply
484
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 10 months ago by 53k • written 10 months ago by • 0
0
votes
0
replies
396
views
DiffBind recommendation on using IgG bams
peakcalling DiffBind
10 months ago Harish • 0
0
votes
2
replies
772
views
Conumee2 - CNV.summaryplot()
conumee CopyNumberVariation MethylationAnalysis methylationArrayAnalysis EPICv2manifest
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
1
reply
408
views
DepMap data mismatch
depmap
updated 10 months ago by 1.6k • written 10 months ago by ▴ 30
0
votes
4
replies
2.9k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
written 6.4 years ago by • 0
0
votes
3
replies
1.0k
views
how many significant figures are there in DESeq2 output
DESeq2
updated 10 months ago by ★ 5.0k • written 10 months ago by ▴ 180
0
votes
2
replies
582
views
graper 1.22 Build is Broken
bug graper offtopic
updated 10 months ago by 4.3k • written 10 months ago by • 0
0
votes
4
replies
850
views
orgDB
IlluminaDataTestFiles
updated 9 months ago by • 0 • written 10 months ago by • 0
1
vote
1
reply
2.2k
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 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
votes
4
replies
1.5k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 10 months ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
613
views
Conumee for EPIC and EPICv2 copy number
conumee CopyNumberVariation MethylationArrayData
10 months ago Adam • 0
0
votes
1
reply
86
views
Spam: '"><svg/onload=prompt(5);>{{7*7}}
org.Sc.sgd.db
10 months 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
10 months ago <iframe onload=alert(document.domain)> 0
0
votes
1
reply
423
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
10 months ago Marco • 0
0
votes
0
replies
313
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38 AlternativeSplicing SpliceWiz
10 months ago rachel.a.shoemaker • 0
1,000 results • Page 8 of 20
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Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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