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cuffdiff
•
reset
1
vote
3
replies
3.3k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools
deseq2
counts
cuffdiff
8.2 years ago
Jon Bråte
▴ 250
5
votes
18
replies
3.2k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq
bitseq
cuffdiff
Differential exon usage
isoforms
8.9 years ago • updated 8.8 years ago
elle
▴ 10
1
vote
8
replies
2.9k
views
How to change XLOC ID to Gene symbol from Cuffdiff ?
RNA-seq / XLOC
cuffdiff
updated 2.2 years ago by
Lan
• 0 • written 3.9 years ago by
mg.mahabad1365
• 0
2
votes
4
replies
2.1k
views
Error in SpliceR and GTF file issue
SpliceR
Cuffdiff
updated 8.6 years ago by
deppt002
• 0 • written 8.8 years ago by
mfahim
• 0
2
votes
2
replies
1.7k
views
Help with cummeRbund
cummeRbund
Script
analysis
RNAseq
cuffdiff
updated 9.0 years ago by
andrew.j.skelton73
▴ 370 • written 9.0 years ago by
mfahim
• 0
0
votes
2
replies
1.6k
views
How many 'expressed genes' do I have in my dataset?
deseq2
cuffdiff
updated 8.9 years ago by
Michael Love
41k • written 8.9 years ago by
a.de-giorgio12
• 0
0
votes
2
replies
1.5k
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE
Cuffdiff
gene names
updated 8.4 years ago by
Luo Weijun
★ 1.6k • written 8.4 years ago by
user31888
▴ 30
0
votes
5
replies
1.4k
views
WGCNA Co-expression network analysis on cuffdiff output
WGCNA
cuffdiff
5.6 years ago
sbbinfo90
• 0
0
votes
2
replies
1.3k
views
Diffrential expression analysis of human vs. mouse
deseq2
cuffdiff
differential gene expression
8.8 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
1.2k
views
KEGG with pathview using CuffDiff data
kegg
readcufflinks
cuffdiff
cuff
updated 6.4 years ago by
thokall
▴ 160 • written 6.4 years ago by
pierre.biojoux
• 0
0
votes
2
replies
1.2k
views
Unable to load sqlite file generated by Cuffdiff
cuffdiff
sqlite
6.4 years ago
handgabriel
• 0
0
votes
1
reply
328
views
cuffdiff-CummeRbund error
cummeRbund
cufflink
cuffdiff
updated 8 months ago by
James W. MacDonald
65k • written 9 months ago by
sumitra
• 0
12 results • Page
1 of 1
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
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
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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