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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 8.9 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
1.7k
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
4.5k
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
939
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 3.9 years ago by
Rory Stark
★ 5.2k • written 3.9 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
767
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
671
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 5.0 years ago by
Wei Shi
★ 3.6k • written 5.0 years ago by
aurel.nagy
▴ 10
1
vote
1
reply
548
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
650
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 14 months ago by
Rory Stark
★ 5.2k • written 14 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
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Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
• 0
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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