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htseqcounts
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0
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4
replies
1.3k
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Normalise counts when tumour samples have normal tissue contamination.
deseq2
deseq
edgeR
rnaseq
htseqcounts
6.1 years ago
Deepali
• 0
0
votes
3
replies
1.8k
views
how to read htseq-count
edger
htseqcounts
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
Bioinformatics
▴ 30
1
vote
1
reply
2.0k
views
Difference between SummarizeOverlaps and HTSeq
R
summarizeoverlaps
htseqcounts
updated 6.4 years ago by
thokall
▴ 160 • written 6.4 years ago by
Walter F. Baumann
▴ 10
1
vote
2
replies
4.2k
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
2.2k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts
SAM
htseqcounts
updated 8 months ago by
Yang Liao
▴ 380 • written 6.9 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 13 months ago by
mhashan.j
▴ 10 • written 7.1 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 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
romsdahl
• 0
0
votes
0
replies
1.0k
views
DEXSeq error: erro in dexseq_count.py
dexseq_count
dexseq
htseqcounts
7.5 years ago
as1023
• 0
0
votes
7
replies
1.6k
views
PCA results different from th same sample but different counting method
deseq2
pca
tximportdata
htseqcounts
updated 7.7 years ago by
Michael Love
41k • written 7.7 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 7.8 years ago by
Gordon Smyth
50k • written 7.8 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 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
sakura.nussbaum
▴ 10
13 results • Page
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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