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HTSeqCounts
•
reset
0
votes
4
replies
1.3k
views
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 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 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 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 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
1 of 1
Recent ...
Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
shuwangxinze1996
• 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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