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htseqcounts
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0
votes
4
replies
1.5k
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Normalise counts when tumour samples have normal tissue contamination.
deseq2
deseq
edgeR
rnaseq
htseqcounts
6.8 years ago
Deepali
• 0
0
votes
3
replies
2.1k
views
how to read htseq-count
edger
htseqcounts
updated 6.8 years ago by
Gordon Smyth
51k • written 6.8 years ago by
Bioinformatics
▴ 30
1
vote
1
reply
2.3k
views
Difference between SummarizeOverlaps and HTSeq
R
summarizeoverlaps
htseqcounts
updated 7.1 years ago by
thokall
▴ 160 • written 7.1 years ago by
Walter F. Baumann
▴ 10
1
vote
2
replies
4.7k
views
Length of 'group' must equal number of columns in 'counts'
htseqcounts
edger
updated 2.1 years ago by
Randy
• 0 • written 7.2 years ago by
mictadlo
▴ 10
3
votes
7
replies
3.5k
views
read counts for each gene for edgeR
edger
htseqcounts
updated 7.2 years ago by
Gordon Smyth
51k • written 7.2 years ago by
mictadlo
▴ 10
2
votes
2
replies
1.3k
views
Why does total unique map not equal to library size?
htseqcounts
star
rnaseq
7.2 years ago
Ahdee
▴ 50
0
votes
5
replies
2.6k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts
SAM
htseqcounts
updated 16 months ago by
Yang Liao
▴ 450 • written 7.5 years ago by
courtney.stairs
• 0
2
votes
4
replies
3.8k
views
Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
chipseq
deseq2
htseqcounts
updated 21 months ago by
mhashan.j
▴ 10 • written 7.8 years ago by
JunLVI
▴ 40
1
vote
1
reply
1.2k
views
RNA-seq: EdgeR's togtags table not correlating to htseq-count's CPM values
edger
htseqcounts
rnaseq
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
romsdahl
• 0
0
votes
0
replies
1.2k
views
DEXSeq error: erro in dexseq_count.py
dexseq_count
dexseq
htseqcounts
8.2 years ago
as1023
• 0
0
votes
7
replies
1.9k
views
PCA results different from th same sample but different counting method
deseq2
pca
tximportdata
htseqcounts
updated 8.4 years ago by
Michael Love
42k • written 8.4 years ago by
jarod_v6@libero.it
▴ 40
1
vote
4
replies
1.9k
views
GOSeq: analysis of unsupported genome after HTseq and DEseq2 - building gene lengths, comparing contrasts and understanding results.
deseq2
goseq
htseqcounts
rnaseq
plant
updated 8.5 years ago by
Gordon Smyth
51k • written 8.5 years ago by
Ben Mansfeld
• 0
1
vote
6
replies
2.1k
views
Error: could not find function "HTSeqCounts"
HTSeq
HTSeqCounts
Could not find function
DEXSeq
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
sakura.nussbaum
▴ 10
13 results • Page
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Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
by
rcreed
• 0
The updated version worked well on my data. Thank you!
Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di
by
James W. MacDonald
67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
Comment: Identical samples after deseq2 batch effect removal
by
Michael Love
42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Comment: Identifying potentially associated gene set to drug response using GSVA
by
Kent
• 0
Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
by
James W. MacDonald
67k
You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…
Votes
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
A: correcting the batch effects in Limma and SVA
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