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cuffdiff
•
reset
5
votes
18
replies
2.2k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq
bitseq
cuffdiff
Differential exon usage
isoforms
7.7 years ago • updated 7.6 years ago
elle
▴ 10
2
votes
4
replies
1.7k
views
Error in SpliceR and GTF file issue
SpliceR
Cuffdiff
updated 7.4 years ago by
deppt002
• 0 • written 7.6 years ago by
mfahim
• 0
2
votes
2
replies
1.3k
views
Help with cummeRbund
cummeRbund
Script
analysis
RNAseq
cuffdiff
updated 7.8 years ago by
andrew.j.skelton73
▴ 360 • written 7.8 years ago by
mfahim
• 0
1
vote
8
replies
1.8k
views
How to change XLOC ID to Gene symbol from Cuffdiff ?
RNA-seq / XLOC
cuffdiff
updated 12 months ago by
Lan
• 0 • written 2.7 years ago by
mg.mahabad1365
• 0
1
vote
3
replies
2.5k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools
deseq2
counts
cuffdiff
7.0 years ago
Jon Bråte
▴ 240
0
votes
2
replies
1.1k
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE
Cuffdiff
gene names
updated 7.2 years ago by
Luo Weijun
★ 1.6k • written 7.2 years ago by
user31888
▴ 30
0
votes
2
replies
1.3k
views
How many 'expressed genes' do I have in my dataset?
deseq2
cuffdiff
updated 7.7 years ago by
Michael Love
39k • written 7.7 years ago by
a.de-giorgio12
• 0
0
votes
1
reply
806
views
KEGG with pathview using CuffDiff data
kegg
readcufflinks
cuffdiff
cuff
updated 5.2 years ago by
thokall
▴ 160 • written 5.2 years ago by
pierre.biojoux
• 0
0
votes
2
replies
819
views
Unable to load sqlite file generated by Cuffdiff
cuffdiff
sqlite
5.2 years ago
handgabriel
• 0
0
votes
5
replies
934
views
WGCNA Co-expression network analysis on cuffdiff output
WGCNA
cuffdiff
4.4 years ago
sbbinfo90
• 0
0
votes
2
replies
965
views
Diffrential expression analysis of human vs. mouse
deseq2
cuffdiff
differential gene expression
7.6 years ago
Assa Yeroslaviz
★ 1.5k
11 results • Page
1 of 1
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR?
by
mohammedtoufiq91
▴ 10
Thank you @gordonsmyth My collaborator asked me to test this pipeline with `egdeR` package. We are interested at gene level analysis only…
Answer: Why in Bioconductor community people rarely upvote questions?
by
Gordon Smyth
47k
I think it is a good idea to start a discussion with correct information. Looking back through Bioconductor Support records, it is not at a…
Comment: How to identify top most variable genes from log2 normalized data?
by
Gordon Smyth
47k
Your code doesn't look right to me. I think you're using order() where sort() would be more appropriate. To order your cpm matrix by row v…
Comment: How to load fasta file with openPrimeR?
by
Santiago Edilberto
• 0
> library(openPrimeR) There are missing/non-functioning external tools. To use the full potential of openPrimeR, please mak…
Answer: Which input file is used for DGEList in EgdeR?
by
Gordon Smyth
47k
I use and recommend featureCounts. Despite all that has been written on this topic, I still think that direct gene counting is faster and m…
Votes
Answer: Which input file is used for DGEList in EgdeR?
Answer: Identifying DEGs using lfcshrink()
Answer: Is this DESeq2 interactions design correct?
Comment: STRINGdb string_db$map error
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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