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Atac
•
reset
1
vote
16
replies
4.8k
views
DiffBind Batch Effect
diffbind
atac
6.9 years ago
niu.shengyong
• 0
8
votes
9
replies
6.1k
views
ChIPseq-style peak calling for paired-end sequencing?
Chipseq
DNAseq
ATAC
bayespeak
narrowpeaks
updated 8.9 years ago by
Gordon Smyth
50k • written 9.0 years ago by
samuel collombet
▴ 140
2
votes
8
replies
1.4k
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma
edger
atac
atac-seq
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
pgugger
▴ 70
0
votes
7
replies
1.8k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 4.9 years ago by
Steve Lianoglou
★ 13k • written 4.9 years ago by
mbasam
• 0
5
votes
7
replies
4.6k
views
Differential binding of ATAC-seq data with no replicates
ATAC
differential binding analysis
no replicates
DEseq2
chromatin
7.1 years ago
BioinfGuru
▴ 30
3
votes
4
replies
2.8k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
g.atla
▴ 10
0
votes
3
replies
948
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 4.7 years ago by
Rory Stark
★ 5.2k • written 4.7 years ago by
rm1238
• 0
1
vote
3
replies
1.2k
views
DiffBind: reverse absolute fold change in dba.report ie. abs(rep$Fold)
diffbind
atac
updated 4.0 years ago by
Rory Stark
★ 5.2k • written 4.0 years ago by
lindsaynhayes
• 0
2
votes
2
replies
2.2k
views
DiffBind for ATAC-seq -- bFullLibrarySize parameter
diffbind
atac
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 5.2 years ago by
paz2005
• 0
0
votes
2
replies
772
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 4.4 years ago by
Gordon Smyth
50k • written 4.4 years ago by
corinne_hutfilz
• 0
0
votes
1
reply
682
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Cynthia
• 0
1
vote
1
reply
2.9k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.1 years ago by
Wei Shi
★ 3.6k • written 5.1 years ago by
aurel.nagy
▴ 10
1
vote
1
reply
553
views
DiffBind t-statistic values
r
DiffBind
ATAC
updated 4.2 years ago by
Rory Stark
★ 5.2k • written 4.2 years ago by
lindsaynhayes
• 0
2
votes
1
reply
1.3k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 5.1 years ago by
Rory Stark
★ 5.2k • written 5.1 years ago by
pgontarz
▴ 10
0
votes
1
reply
658
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 14 months ago by
Rory Stark
★ 5.2k • written 15 months ago by
Hadar
• 0
0
votes
1
reply
1.4k
views
Using Diffbind on ATAC data - adapter offset issue
Diffbind
Atac
adapters
updated 7.1 years ago by
Rory Stark
★ 5.2k • written 7.1 years ago by
BioinfGuru
▴ 30
16 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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