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Cuffdiff
•
reset
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
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
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
1.6k
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
1.2k
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
1
reply
327
views
cuffdiff-CummeRbund error
cummeRbund
cufflink
cuffdiff
updated 8 months ago by
James W. MacDonald
65k • written 9 months ago by
sumitra
• 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: 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?
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
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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