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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
944
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$Fold)
diffbind
atac
updated 3.9 years ago by
Rory Stark
★ 5.2k • written 4.0 years ago by
lindsaynhayes
• 0
2
votes
2
replies
2.2k
views
DiffBind for ATAC-seq -- bFullLibrarySize parameter
diffbind
atac
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 5.2 years ago by
paz2005
• 0
0
votes
2
replies
769
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 4.4 years ago by
Gordon Smyth
50k • written 4.4 years ago by
corinne_hutfilz
• 0
0
votes
1
reply
678
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Cynthia
• 0
1
vote
1
reply
2.9k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.1 years ago by
Wei Shi
★ 3.6k • written 5.1 years ago by
aurel.nagy
▴ 10
1
vote
1
reply
552
views
DiffBind t-statistic values
r
DiffBind
ATAC
updated 4.2 years ago by
Rory Stark
★ 5.2k • written 4.2 years ago by
lindsaynhayes
• 0
2
votes
1
reply
1.3k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 5.1 years ago by
Rory Stark
★ 5.2k • written 5.1 years ago by
pgontarz
▴ 10
0
votes
1
reply
656
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 14 months ago by
Rory Stark
★ 5.2k • written 15 months ago by
Hadar
• 0
0
votes
1
reply
1.4k
views
Using Diffbind on ATAC data - adapter offset issue
Diffbind
Atac
adapters
updated 7.1 years ago by
Rory Stark
★ 5.2k • written 7.1 years ago by
BioinfGuru
▴ 30
16 results • Page
1 of 1
Recent ...
Replies
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Votes
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
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Rory Stark
★ 5.2k
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tangming2005
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