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cuffdiff
•
reset
5
votes
18
replies
3.1k
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
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
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
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
0
votes
1
reply
323
views
cuffdiff-CummeRbund error
cummeRbund
cufflink
cuffdiff
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
sumitra
• 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
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
1.5k
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
2
replies
1.2k
views
Unable to load sqlite file generated by Cuffdiff
cuffdiff
sqlite
6.4 years ago
handgabriel
• 0
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
12 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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