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htseqtools
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HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools
deseq2
counts
cuffdiff
8.2 years ago
Jon Bråte
▴ 250
0
votes
4
replies
1.8k
views
htSeqTools errors
Coverage
htSeqTools
Coverage
htSeqTools
updated 12.2 years ago by
Valerie Obenchain
★ 6.8k • written 12.2 years ago by
Juan L. Mateo
▴ 80
0
votes
1
reply
1.6k
views
GenomicRanges requires a IRanges version not available in the repository
GenomicRanges
htSeqTools
GenomicRanges
htSeqTools
updated 12.2 years ago by
Vincent J. Carey, Jr.
6.7k • written 12.2 years ago by
Juan L. Mateo
▴ 80
0
votes
2
replies
1.2k
views
htSeqTools - naming RangedData objects?
htSeqTools
ASSIGN
htSeqTools
ASSIGN
updated 12.3 years ago by
Michael Lawrence
★ 11k • written 12.3 years ago by
Ian D.
▴ 70
0
votes
3
replies
1.0k
views
Which library now contains the ssdCoverage command that used to be found in the htseqtools package for R version 4.0.1 ?
Deprecation
chipseq
htseqtools
Bioconductor
updated 3.1 years ago by
Basti
▴ 780 • written 3.2 years ago by
Mick
• 0
0
votes
0
replies
945
views
htSeqTools: using GRanges and GRangesList
convert
htSeqTools
convert
htSeqTools
12.3 years ago
Oscar Reina
▴ 20
0
votes
1
reply
794
views
htSeqTools - filtered reads > BED?
IRanges
htSeqTools
IRanges
htSeqTools
updated 12.3 years ago by
Michael Lawrence
★ 11k • written 12.3 years ago by
Ian D.
▴ 70
7 results • Page
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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