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atac
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565
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FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
9 months ago
Raghad
• 0
0
votes
1
reply
1.1k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
Cynthia
• 0
0
votes
1
reply
917
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 2.0 years ago by
Rory Stark
★ 5.2k • written 2.0 years ago by
Hadar
• 0
1
vote
3
replies
1.6k
views
DiffBind: reverse absolute fold change in dba.report ie. abs(rep$Fold)
diffbind
atac
updated 4.8 years ago by
Rory Stark
★ 5.2k • written 4.8 years ago by
lindsaynhayes
• 0
1
vote
1
reply
709
views
DiffBind t-statistic values
r
DiffBind
ATAC
updated 5.0 years ago by
Rory Stark
★ 5.2k • written 5.0 years ago by
lindsaynhayes
• 0
2
votes
8
replies
1.9k
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma
edger
atac
atac-seq
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
pgugger
▴ 70
0
votes
2
replies
962
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 5.2 years ago by
Gordon Smyth
52k • written 5.2 years ago by
corinne_hutfilz
• 0
0
votes
3
replies
1.2k
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 5.5 years ago by
Rory Stark
★ 5.2k • written 5.5 years ago by
rm1238
• 0
0
votes
7
replies
2.2k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 5.7 years ago by
Steve Lianoglou
★ 13k • written 5.7 years ago by
mbasam
• 0
1
vote
1
reply
3.7k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.9 years ago by
Wei Shi
★ 3.6k • written 5.9 years ago by
aurel.nagy
▴ 10
2
votes
1
reply
1.7k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 5.9 years ago by
Rory Stark
★ 5.2k • written 5.9 years ago by
pgontarz
▴ 10
2
votes
2
replies
2.6k
views
DiffBind for ATAC-seq -- bFullLibrarySize parameter
diffbind
atac
updated 6.0 years ago by
Rory Stark
★ 5.2k • written 6.0 years ago by
paz2005
• 0
6
votes
16
replies
6.1k
views
DiffBind Batch Effect
diffbind
atac
7.7 years ago
niu.shengyong
▴ 10
5
votes
7
replies
5.1k
views
Differential binding of ATAC-seq data with no replicates
ATAC
differential binding analysis
no replicates
DEseq2
chromatin
7.9 years ago
BioinfGuru
▴ 70
0
votes
1
reply
1.6k
views
Using Diffbind on ATAC data - adapter offset issue
Diffbind
Atac
adapters
updated 7.9 years ago by
Rory Stark
★ 5.2k • written 7.9 years ago by
BioinfGuru
▴ 70
3
votes
4
replies
3.3k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
g.atla
▴ 10
8
votes
9
replies
6.8k
views
ChIPseq-style peak calling for paired-end sequencing?
Chipseq
DNAseq
ATAC
bayespeak
narrowpeaks
updated 9.7 years ago by
Gordon Smyth
52k • written 9.8 years ago by
samuel collombet
▴ 140
17 results • Page
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shepherl
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It seems likely this was installed as an admin account and a user account would not be able to update. Someone with admin access should run…
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Answer: batch effect removal for agilent microarray data
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Since `BiocManager::install` is a wrapper around `install.packages` you should be able to use the dependencies argument. Default is the de…
Comment: For some reason I can't update BiocManager to 3.20
by
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• 0
Sorry i apologize for the delay. Thank you very much for the answer. I have two supervisers and the one who knows about the computer is com…
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Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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