0
votes
0
replies
24
views
best way to grouping GSM belonging to different datasets (with different platforms) and compare differential gene expression
GEOquery
1 day ago Alexander • 0
0
votes
1
reply
260
views
CpGs with genomic positions greater than the chromosome size in EPICv2?
EPICv2 EPICv2manifest
updated 1 day ago by 68k • written 2 days ago by • 0
1
vote
3
replies
272
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
updated 2 days ago by 68k • written 2 days ago by • 0
0
votes
0
replies
35
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Error in cnetplot
enrichplot clusterProfiler
3 days ago Ayesha • 0
4
votes
5
replies
892
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Using TPM from tximport of Salmon output for singscore
singscore
4 days ago • updated 1 day ago Kent • 0
5
votes
3
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727
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 3 days ago by 52k • written 4 days ago by ▴ 10
2
votes
10
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3.8k
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Problem at champ.load
ChAMPdata ChAMP
updated 4 days ago by • 0 • written 23 months ago by • 0
0
votes
1
reply
159
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GAGE kegg.gsets() self-signed certificate error
gageData gage
4 days ago • updated 2 days ago Lucas • 0
0
votes
2
replies
229
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myvariant error
myvariant getVariants
updated 4 days ago by • 0 • written 19 days ago by • 0
0
votes
4
replies
388
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 5 days ago by • 0
0
votes
0
replies
28
views
DiffBind multi-tissue comparison
DiffBind
5 days ago lryrainche • 0
1
vote
2
replies
362
views
affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 5 days ago by 68k • written 7 days ago by • 0
0
votes
4
replies
225
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Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm10.knownGene
5 days ago • updated 4 days ago Wolfgang RAFFELSBERGER ▴ 140
0
votes
0
replies
63
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
6 days ago GT • 0
1
vote
1
reply
588
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 8 days ago by 68k • written 8 days ago by • 0
0
votes
0
replies
35
views
Limma: twin study with mono & dizygotic, discordant and concordant pairs
twins limma formula design
8 days ago Geoff • 0
0
votes
2
replies
587
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Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
9 days ago • updated 3 days ago DavideSant • 0
2
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2
replies
1.1k
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Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
11 days ago • updated 5 days ago Elizabeth • 0
1
vote
2
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1.2k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
11 days ago • updated 10 days ago Luca • 0
0
votes
1
reply
261
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Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 10 days ago by 68k • written 11 days ago by • 0
1
vote
3
replies
789
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac AnnotationHub
written 12 days ago by ▴ 110
0
votes
1
reply
159
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Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling RiboSeq
updated 11 days ago by 4.1k • written 11 days ago by • 0
0
votes
4
replies
494
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Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
16 days ago • updated 5 days ago Nicholas • 0
0
votes
1
reply
265
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Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools BiomedicalInformatics GeneExpression
updated 12 days ago by 68k • written 13 days ago by • 0
0
votes
0
replies
45
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Simple confidence intervall Gviz
Gviz
12 days ago William • 0
1
vote
3
replies
19k
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Warning message---BiocManager::install
BiocManager::install
written 3.6 years ago by • 0
0
votes
2
replies
360
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org.Hs.eg.db issue
org.Hs.eg.db
written 10 weeks ago by • 0
0
votes
2
replies
385
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 5 days ago by 43k • written 13 days ago by ▴ 20
1
vote
2
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736
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Differential expression of proteins using somascan data
somascan limma
written 15 days ago by • 0
4
votes
5
replies
923
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 3 days ago by • 0 • written 17 days ago by • 0
0
votes
1
reply
220
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library org.Hs.eg.db failing to install
org.Hs.eg.db
updated 16 days ago by 68k • written 16 days ago by • 0
0
votes
1
reply
178
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 16 days ago by 43k • written 17 days ago by • 0
0
votes
7
replies
2.4k
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DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 16 days ago by • 0 • written 23 months ago by • 0
0
votes
2
replies
317
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Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
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17 days ago • updated 16 days ago Yao Lipu • 0
0
votes
1
reply
191
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Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 18 days ago by 52k • written 18 days ago by • 0
0
votes
0
replies
73
views
DiffBind recommendation on using IgG bams
peakcalling DiffBind
18 days ago Harish • 0
0
votes
2
replies
180
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Conumee2 - CNV.summaryplot()
conumee CopyNumberVariation MethylationAnalysis methylationArrayAnalysis EPICv2manifest
updated 18 days ago by 68k • written 18 days ago by • 0
0
votes
1
reply
148
views
DepMap data mismatch
depmap
updated 18 days ago by 1.6k • written 18 days ago by ▴ 30
0
votes
4
replies
2.4k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
written 5.6 years ago by • 0
0
votes
3
replies
599
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how many significant figures are there in DESeq2 output
DESeq2
updated 20 days ago by ★ 4.7k • written 22 days ago by ▴ 180
0
votes
0
replies
96
views
News: GSEA in R/Bioconductor course
GSEABenchmarkeR pairedGSEA GeneSetEnrichment
22 days ago info ▴ 10
0
votes
2
replies
231
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graper 1.22 Build is Broken
bug graper offtopic
updated 22 days ago by 4.1k • written 22 days ago by • 0
0
votes
1
reply
88
views
cannot download atena annotation for human
atena
22 days ago Davide • 0
0
votes
4
replies
394
views
orgDB
IlluminaDataTestFiles
updated 12 days ago by • 0 • written 22 days ago by • 0
1
vote
1
reply
678
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 22 days ago by ★ 4.7k • written 22 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 17 days ago by • 0 • written 23 days ago by • 0
0
votes
1
reply
193
views
Conumee for EPIC and EPICv2 copy number
conumee CopyNumberVariation MethylationArrayData
23 days ago • updated 22 days ago Adam • 0
0
votes
1
reply
85
views
Spam: '"><svg/onload=prompt(5);>{{7*7}}
org.Sc.sgd.db
23 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
23 days ago <iframe onload=alert(document.domain)> 0
0
votes
1
reply
180
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
23 days ago • updated 22 days ago Marco • 0
46,406 results • Page 1 of 929
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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