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37
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CpGs with genomic positions greater than the chromosome size in EPICv2?
EPICv2 EPICv2manifest
updated 1 hour ago by 68k • written 1 day ago by • 0
1
vote
3
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239
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
updated 22 hours ago by 68k • written 1 day ago by • 0
0
votes
0
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30
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Error in cnetplot
enrichplot clusterProfiler
2 days ago Ayesha • 0
4
votes
5
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442
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Using TPM from tximport of Salmon output for singscore
singscore
3 days ago • updated 3 hours ago Kent • 0
5
votes
3
replies
709
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 1 day ago by 52k • written 2 days ago by ▴ 10
2
votes
10
replies
3.8k
views
Problem at champ.load
ChAMPdata ChAMP
updated 2 days ago by • 0 • written 23 months ago by • 0
0
votes
1
reply
152
views
GAGE kegg.gsets() self-signed certificate error
gageData gage
2 days ago • updated 21 hours ago Lucas • 0
0
votes
2
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226
views
myvariant error
myvariant getVariants
updated 3 days ago by • 0 • written 18 days ago by • 0
0
votes
4
replies
370
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 3 days ago by • 0
0
votes
0
replies
25
views
DiffBind multi-tissue comparison
DiffBind
3 days ago lryrainche • 0
1
vote
2
replies
358
views
affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 4 days ago by 68k • written 5 days ago by • 0
0
votes
4
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220
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Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm10.knownGene
4 days ago • updated 3 days ago Wolfgang RAFFELSBERGER ▴ 140
0
votes
0
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58
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
4 days ago GT • 0
0
votes
1
reply
393
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 6 days ago by 68k • written 7 days ago by • 0
0
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0
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32
views
Limma: twin study with mono & dizygotic, discordant and concordant pairs
twins limma formula design
6 days ago Geoff • 0
0
votes
2
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583
views
Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
8 days ago • updated 2 days ago DavideSant • 0
2
votes
2
replies
1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
10 days ago • updated 4 days ago Elizabeth • 0
1
vote
2
replies
1.2k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
9 days ago • updated 8 days ago Luca • 0
0
votes
1
reply
260
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 9 days ago by 68k • written 9 days ago by • 0
1
vote
3
replies
784
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac AnnotationHub
written 10 days ago by ▴ 110
0
votes
1
reply
158
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling RiboSeq
updated 10 days ago by 4.1k • written 10 days ago by • 0
0
votes
4
replies
490
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
14 days ago • updated 4 days ago Nicholas • 0
0
votes
1
reply
262
views
Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools BiomedicalInformatics GeneExpression
updated 11 days ago by 68k • written 11 days ago by • 0
0
votes
0
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44
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Simple confidence intervall Gviz
Gviz
11 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
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358
views
org.Hs.eg.db issue
org.Hs.eg.db
written 9 weeks ago by • 0
0
votes
2
replies
372
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 4 days ago by 43k • written 12 days ago by ▴ 20
1
vote
2
replies
725
views
Differential expression of proteins using somascan data
somascan limma
written 13 days ago by • 0
4
votes
5
replies
914
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 2 days ago by • 0 • written 15 days ago by • 0
0
votes
1
reply
216
views
library org.Hs.eg.db failing to install
org.Hs.eg.db
updated 14 days ago by 68k • written 14 days ago by • 0
0
votes
1
reply
174
views
DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 14 days ago by 43k • written 15 days ago by • 0
0
votes
7
replies
2.4k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 14 days ago by • 0 • written 23 months ago by • 0
0
votes
2
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315
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Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
hta20transcriptcluster.db org.Sc.sgd.db HTA2.0 MicroRNAArrayData
15 days ago • updated 14 days ago Yao Lipu • 0
0
votes
1
reply
190
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 16 days ago by 52k • written 16 days ago by • 0
0
votes
0
replies
68
views
DiffBind recommendation on using IgG bams
peakcalling DiffBind
16 days ago Harish • 0
0
votes
2
replies
178
views
Conumee2 - CNV.summaryplot()
conumee CopyNumberVariation MethylationAnalysis methylationArrayAnalysis EPICv2manifest
updated 17 days ago by 68k • written 17 days ago by • 0
0
votes
1
reply
145
views
DepMap data mismatch
depmap
updated 17 days ago by 1.6k • written 17 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
596
views
how many significant figures are there in DESeq2 output
DESeq2
updated 19 days ago by ★ 4.7k • written 20 days ago by ▴ 180
0
votes
0
replies
92
views
News: GSEA in R/Bioconductor course
GSEABenchmarkeR pairedGSEA GeneSetEnrichment
21 days ago info ▴ 10
0
votes
2
replies
229
views
graper 1.22 Build is Broken
bug graper offtopic
updated 21 days ago by 4.1k • written 21 days ago by • 0
0
votes
1
reply
87
views
cannot download atena annotation for human
atena
21 days ago Davide • 0
0
votes
4
replies
390
views
orgDB
IlluminaDataTestFiles
updated 10 days ago by • 0 • written 21 days ago by • 0
1
vote
1
reply
650
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 21 days ago by ★ 4.7k • written 21 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 16 days ago by • 0 • written 21 days ago by • 0
0
votes
1
reply
189
views
Conumee for EPIC and EPICv2 copy number
conumee CopyNumberVariation MethylationArrayData
21 days ago • updated 20 days ago Adam • 0
0
votes
1
reply
85
views
Spam: '"><svg/onload=prompt(5);>{{7*7}}
org.Sc.sgd.db
21 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
21 days ago <iframe onload=alert(document.domain)> 0
0
votes
1
reply
175
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
21 days ago • updated 20 days ago Marco • 0
0
votes
0
replies
47
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38 AlternativeSplicing SpliceWiz
21 days ago rachel.a.shoemaker • 0
46,405 results • Page 1 of 929
Recent ...
Replies
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 …
Comment: deseq2 lfc shrinkage with few DEGs by Michael Love 43k
Agree with your edit.
Votes
Comment: Using TPM from tximport of Salmon output for singscore
Answer: Using TPM from tximport of Salmon output for singscore
Comment: deseq2 lfc shrinkage with few DEGs
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
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