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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
8.8 years ago
elle
▴ 10
2
votes
4
replies
2.0k
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
1.6k
views
Help with cummeRbund
cummeRbund
Script
analysis
RNAseq
cuffdiff
updated 8.9 years ago by
andrew.j.skelton73
▴ 370 • written 8.9 years ago by
mfahim
• 0
1
vote
3
replies
3.2k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools
deseq2
counts
cuffdiff
8.1 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
1.4k
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE
Cuffdiff
gene names
updated 8.3 years ago by
Luo Weijun
★ 1.6k • written 8.3 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 8.8 years ago by
Michael Love
41k • written 8.8 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
5.5 years ago
sbbinfo90
• 0
0
votes
1
reply
299
views
cuffdiff-CummeRbund error
cummeRbund
cufflink
cuffdiff
updated 7 months ago by
James W. MacDonald
65k • written 8 months ago by
sumitra
• 0
0
votes
2
replies
1.3k
views
Diffrential expression analysis of human vs. mouse
deseq2
cuffdiff
differential gene expression
8.7 years ago
Assa Yeroslaviz
★ 1.5k
12 results • Page
1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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