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atac
•
reset
0
votes
0
replies
1.1k
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
20 months ago
Raghad
• 0
0
votes
1
reply
1.7k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 2.8 years ago by
James W. MacDonald
68k • written 2.8 years ago by
Cynthia
• 0
0
votes
1
reply
1.3k
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 2.9 years ago by
Rory Stark
★ 5.2k • written 3.0 years ago by
Hadar
• 0
1
vote
3
replies
1.8k
views
DiffBind: reverse absolute fold change in dba.report ie. abs(rep$Fold)
diffbind
atac
updated 5.7 years ago by
Rory Stark
★ 5.2k • written 5.7 years ago by
lindsaynhayes
• 0
1
vote
1
reply
885
views
DiffBind t-statistic values
r
DiffBind
ATAC
updated 5.9 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
lindsaynhayes
• 0
2
votes
8
replies
2.5k
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma
edger
atac
atac-seq
updated 5.9 years ago by
Aaron Lun
★ 29k • written 5.9 years ago by
pgugger
▴ 70
0
votes
2
replies
1.3k
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 6.1 years ago by
Gordon Smyth
53k • written 6.1 years ago by
corinne_hutfilz
• 0
0
votes
3
replies
1.4k
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 6.4 years ago by
Rory Stark
★ 5.2k • written 6.4 years ago by
rm1238
• 0
0
votes
7
replies
2.6k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 6.6 years ago by
Steve Lianoglou
★ 13k • written 6.6 years ago by
mbasam
• 0
1
vote
1
reply
4.3k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 6.8 years ago by
Wei Shi
★ 3.6k • written 6.8 years ago by
aurel.nagy
▴ 10
2
votes
1
reply
2.0k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 6.8 years ago by
Rory Stark
★ 5.2k • written 6.8 years ago by
pgontarz
▴ 10
2
votes
2
replies
2.9k
views
DiffBind for ATAC-seq -- bFullLibrarySize parameter
diffbind
atac
updated 6.9 years ago by
Rory Stark
★ 5.2k • written 6.9 years ago by
paz2005
• 0
6
votes
16
replies
7.1k
views
DiffBind Batch Effect
diffbind
atac
8.6 years ago
niu.shengyong
▴ 10
5
votes
7
replies
5.7k
views
Differential binding of ATAC-seq data with no replicates
ATAC
differential binding analysis
no replicates
DEseq2
chromatin
8.8 years ago
BioinfGuru
▴ 70
0
votes
1
reply
1.8k
views
Using Diffbind on ATAC data - adapter offset issue
Diffbind
Atac
adapters
updated 8.8 years ago by
Rory Stark
★ 5.2k • written 8.8 years ago by
BioinfGuru
▴ 70
3
votes
4
replies
3.8k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 8.9 years ago by
Michael Love
43k • written 8.9 years ago by
g.atla
▴ 10
8
votes
9
replies
7.4k
views
ChIPseq-style peak calling for paired-end sequencing?
Chipseq
DNAseq
ATAC
bayespeak
narrowpeaks
updated 10.6 years ago by
Gordon Smyth
53k • written 10.7 years ago by
samuel collombet
▴ 140
17 results • Page
1 of 1
Recent ...
Replies
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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