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ChIPSeq
•
reset
0
votes
0
replies
104
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
7 weeks ago
nilanjanamani88
• 0
1
vote
3
replies
318
views
Big differences between biological replicates makes DESeq2 result 0
chipseq
DifferentialMethylation
DESeq2
updated 8 weeks ago by
Michael Love
41k • written 9 weeks ago by
rebw25
• 0
0
votes
0
replies
126
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
10 weeks ago
frueher
• 0
0
votes
0
replies
285
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
4 months ago
jared.andrews07
▴ 30
1
vote
1
reply
392
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
lin.pei26
• 0
0
votes
0
replies
253
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno
ChIPSeq
MotifDiscovery
6 months ago
franciscrick41
• 0
2
votes
14
replies
1.0k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno
ChIPSeq
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
Jerina
▴ 10
0
votes
5
replies
2.7k
views
diffbind
DiffBind
chipseq
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
ANAMIKA
• 0
1
vote
4
replies
922
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 10 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
lin.pei26
• 0
0
votes
2
replies
560
views
annotate peaks using a custom genome
ChIPSeq
annotate
ChIPpeakAnno
updated 11 months ago by
Kai Hu
▴ 70 • written 11 months ago by
C T
▴ 140
5
votes
8
replies
935
views
Help with error install csaw
ChIPSeq
ATACSeq
updated 11 months ago by
nekisaf309
• 0 • written 12 months ago by
Chris
• 0
0
votes
1
reply
1.1k
views
diffBind analysis: only one replicate
diffbind
chipseq
updated 10 months ago by
lin.pei26
• 0 • written 4.6 years ago by
danielaperry2015
• 0
1
vote
3
replies
1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind
R
chipseq
updated 3 months ago by
Rory Stark
★ 5.1k • written 6.5 years ago by
kyliecode
• 0
13 results • Page
1 of 1
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Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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