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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 2.5 years ago by
Basti
▴ 720 • written 2.5 years ago by
Mick
• 0
1
vote
3
replies
2.9k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools
deseq2
counts
cuffdiff
7.6 years ago
Jon Bråte
▴ 250
0
votes
4
replies
1.5k
views
htSeqTools errors
Coverage
htSeqTools
Coverage
htSeqTools
updated 11.6 years ago by
Valerie Obenchain
★ 6.8k • written 11.6 years ago by
Juan L. Mateo
▴ 80
0
votes
1
reply
1.5k
views
GenomicRanges requires a IRanges version not available in the repository
GenomicRanges
htSeqTools
GenomicRanges
htSeqTools
updated 11.6 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.6 years ago by
Juan L. Mateo
▴ 80
0
votes
1
reply
687
views
htSeqTools - filtered reads > BED?
IRanges
htSeqTools
IRanges
htSeqTools
updated 11.7 years ago by
Michael Lawrence
11k • written 11.7 years ago by
Ian Donaldson
▴ 70
0
votes
0
replies
827
views
htSeqTools: using GRanges and GRangesList
convert
htSeqTools
convert
htSeqTools
11.7 years ago
Oscar Reina
▴ 20
0
votes
2
replies
1.1k
views
htSeqTools - naming RangedData objects?
htSeqTools
ASSIGN
htSeqTools
ASSIGN
updated 11.7 years ago by
Michael Lawrence
11k • written 11.7 years ago by
Ian Donaldson
▴ 70
7 results • Page
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Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
Rockbar
• 0
When I apply the model.matrix approach for getting the contrasts, the code > mod_mat <- model.matrix(design(dds), colData(dds)) > CondA.t…
Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
Rockbar
• 0
Yes, I agree, the correct contrast setting is quite challenging. The vignette says >contrast: a list of 2 character vectors: the names of…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Advantage and disadvantage depends on the aim, what you plan to do with them (testing, plots, etc.). lengthScaledTPM puts back *in* the ge…
Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
James W. MacDonald
63k
No, putting -1 in the design matrix is a cell means model, which is the opposite. If you used `~ Cond + Cond:Time`, you would specify a fac…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Christian
• 0
Thank you for the response and apologies for my late reply. I think I´m starting getting the concept now. The hints with the cqn is quite …
Votes
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Remove duplicates of colData in TreeSummarizedExperiment
Answer: Remove duplicates of colData in TreeSummarizedExperiment
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