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chipseq
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0
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100
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
7 weeks ago
nilanjanamani88
• 0
1
vote
3
replies
317
views
Big differences between biological replicates makes DESeq2 result 0
chipseq
DifferentialMethylation
DESeq2
updated 7 weeks ago by
Michael Love
41k • written 8 weeks ago by
rebw25
• 0
0
votes
0
replies
125
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
9 weeks ago
frueher
• 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
0
votes
0
replies
282
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
391
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
251
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
921
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 9 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
lin.pei26
• 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
0
votes
2
replies
558
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
932
views
Help with error install csaw
ChIPSeq
ATACSeq
updated 11 months ago by
nekisaf309
• 0 • written 12 months ago by
Chris
• 0
13 results • Page
1 of 1
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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
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
Answer: Microarray Limma Model fitting and DEG
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