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htseqtools
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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 4.1 years ago by
Basti
▴ 780 • written 4.1 years ago by
Mick
• 0
1
vote
3
replies
4.0k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools
deseq2
counts
cuffdiff
9.2 years ago
Jon Bråte
▴ 260
0
votes
4
replies
2.1k
views
htSeqTools errors
Coverage
htSeqTools
Coverage
htSeqTools
updated 13.2 years ago by
Valerie Obenchain
★ 6.8k • written 13.2 years ago by
Juan L. Mateo
▴ 80
0
votes
1
reply
1.8k
views
GenomicRanges requires a IRanges version not available in the repository
GenomicRanges
htSeqTools
GenomicRanges
htSeqTools
updated 13.2 years ago by
Vincent J. Carey, Jr.
6.7k • written 13.2 years ago by
Juan L. Mateo
▴ 80
0
votes
1
reply
984
views
htSeqTools - filtered reads > BED?
IRanges
htSeqTools
IRanges
htSeqTools
updated 13.3 years ago by
Michael Lawrence
★ 11k • written 13.3 years ago by
Ian D.
▴ 70
0
votes
0
replies
1.1k
views
htSeqTools: using GRanges and GRangesList
convert
htSeqTools
convert
htSeqTools
13.3 years ago
Oscar Reina
▴ 20
0
votes
2
replies
1.4k
views
htSeqTools - naming RangedData objects?
htSeqTools
ASSIGN
htSeqTools
ASSIGN
updated 13.3 years ago by
Michael Lawrence
★ 11k • written 13.3 years ago by
Ian D.
▴ 70
7 results • Page
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Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
donnycrimson
• 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Comment: CluserProfiler message "No gene can be mapped"
by
Carolina
• 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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