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htseqcounts
•
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0
votes
4
replies
1.3k
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Normalise counts when tumour samples have normal tissue contamination.
deseq2
deseq
edgeR
rnaseq
htseqcounts
6.2 years ago
Deepali
• 0
0
votes
3
replies
1.9k
views
how to read htseq-count
edger
htseqcounts
updated 6.3 years ago by
Gordon Smyth
50k • written 6.3 years ago by
Bioinformatics
▴ 30
1
vote
1
reply
2.0k
views
Difference between SummarizeOverlaps and HTSeq
R
summarizeoverlaps
htseqcounts
updated 6.5 years ago by
thokall
▴ 160 • written 6.5 years ago by
Walter F. Baumann
▴ 10
1
vote
2
replies
4.3k
views
Length of 'group' must equal number of columns in 'counts'
htseqcounts
edger
updated 18 months ago by
Randy
• 0 • written 6.6 years ago by
mictadlo
▴ 10
3
votes
7
replies
3.2k
views
read counts for each gene for edgeR
edger
htseqcounts
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
mictadlo
▴ 10
2
votes
2
replies
1.1k
views
Why does total unique map not equal to library size?
htseqcounts
star
rnaseq
6.6 years ago
Ahdee
▴ 50
0
votes
5
replies
2.3k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts
SAM
htseqcounts
updated 9 months ago by
Yang Liao
▴ 380 • written 7.0 years ago by
courtney.stairs
• 0
2
votes
4
replies
3.4k
views
Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
chipseq
deseq2
htseqcounts
updated 14 months ago by
mhashan.j
▴ 10 • written 7.2 years ago by
JunLVI
▴ 40
1
vote
1
reply
1.1k
views
RNA-seq: EdgeR's togtags table not correlating to htseq-count's CPM values
edger
htseqcounts
rnaseq
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
romsdahl
• 0
0
votes
0
replies
1.1k
views
DEXSeq error: erro in dexseq_count.py
dexseq_count
dexseq
htseqcounts
7.6 years ago
as1023
• 0
0
votes
7
replies
1.7k
views
PCA results different from th same sample but different counting method
deseq2
pca
tximportdata
htseqcounts
updated 7.8 years ago by
Michael Love
41k • written 7.8 years ago by
jarod_v6@libero.it
▴ 40
1
vote
4
replies
1.7k
views
GOSeq: analysis of unsupported genome after HTseq and DEseq2 - building gene lengths, comparing contrasts and understanding results.
deseq2
goseq
htseqcounts
rnaseq
plant
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
Ben Mansfeld
• 0
1
vote
6
replies
1.9k
views
Error: could not find function "HTSeqCounts"
HTSeq
HTSeqCounts
Could not find function
DEXSeq
updated 8.0 years ago by
Martin Morgan
25k • written 8.0 years ago by
sakura.nussbaum
▴ 10
13 results • Page
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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