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HTSeqCounts
•
reset
0
votes
4
replies
1.7k
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Normalise counts when tumour samples have normal tissue contamination.
deseq2
deseq
edgeR
rnaseq
htseqcounts
7.2 years ago
Deepali
• 0
0
votes
3
replies
2.3k
views
how to read htseq-count
edger
htseqcounts
updated 7.3 years ago by
Gordon Smyth
52k • written 7.3 years ago by
Bioinformatics
▴ 30
1
vote
1
reply
2.6k
views
Difference between SummarizeOverlaps and HTSeq
R
summarizeoverlaps
htseqcounts
updated 7.5 years ago by
thokall
▴ 160 • written 7.5 years ago by
Walter F. Baumann
▴ 10
1
vote
2
replies
4.9k
views
Length of 'group' must equal number of columns in 'counts'
htseqcounts
edger
updated 2.6 years ago by
Randy
• 0 • written 7.6 years ago by
mictadlo
▴ 10
3
votes
7
replies
3.7k
views
read counts for each gene for edgeR
edger
htseqcounts
updated 7.6 years ago by
Gordon Smyth
52k • written 7.6 years ago by
mictadlo
▴ 10
2
votes
2
replies
1.4k
views
Why does total unique map not equal to library size?
htseqcounts
star
rnaseq
7.6 years ago
Ahdee
▴ 60
0
votes
5
replies
2.8k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts
SAM
htseqcounts
updated 21 months ago by
Yang Liao
▴ 450 • written 8.0 years ago by
courtney.stairs
• 0
2
votes
4
replies
4.0k
views
Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
chipseq
deseq2
htseqcounts
updated 2.2 years ago by
mhashan.j
▴ 10 • written 8.2 years ago by
JunLVI
▴ 40
1
vote
1
reply
1.3k
views
RNA-seq: EdgeR's togtags table not correlating to htseq-count's CPM values
edger
htseqcounts
rnaseq
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
romsdahl
• 0
0
votes
0
replies
1.3k
views
DEXSeq error: erro in dexseq_count.py
dexseq_count
dexseq
htseqcounts
8.6 years ago
as1023
• 0
0
votes
7
replies
2.1k
views
PCA results different from th same sample but different counting method
deseq2
pca
tximportdata
htseqcounts
updated 8.8 years ago by
Michael Love
43k • written 8.8 years ago by
jarod_v6@libero.it
▴ 40
1
vote
4
replies
2.1k
views
GOSeq: analysis of unsupported genome after HTseq and DEseq2 - building gene lengths, comparing contrasts and understanding results.
deseq2
goseq
htseqcounts
rnaseq
plant
updated 8.9 years ago by
Gordon Smyth
52k • written 8.9 years ago by
Ben Mansfeld
• 0
1
vote
6
replies
2.3k
views
Error: could not find function "HTSeqCounts"
HTSeq
HTSeqCounts
Could not find function
DEXSeq
updated 9.0 years ago by
Martin Morgan
25k • written 9.0 years ago by
sakura.nussbaum
▴ 10
13 results • Page
1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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