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htseqtools
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3.3k
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HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools
deseq2
counts
cuffdiff
8.3 years ago
Jon Bråte
▴ 250
0
votes
1
reply
799
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
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
4
replies
1.8k
views
htSeqTools errors
Coverage
htSeqTools
Coverage
htSeqTools
updated 12.2 years ago by
Valerie Obenchain
★ 6.8k • written 12.3 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 12.3 years ago by
Vincent J. Carey, Jr.
6.7k • written 12.3 years ago by
Juan L. Mateo
▴ 80
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 3.2 years ago by
Basti
▴ 780 • written 3.2 years ago by
Mick
• 0
0
votes
0
replies
949
views
htSeqTools: using GRanges and GRangesList
convert
htSeqTools
convert
htSeqTools
12.3 years ago
Oscar Reina
▴ 20
7 results • Page
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Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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