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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 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 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 4.8 years ago by
Steve Lianoglou
★ 13k • written 4.8 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
▴ 20
3
votes
4
replies
2.8k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 7.1 years ago by
Michael Love
41k • written 7.2 years ago by
g.atla
▴ 10
0
votes
3
replies
927
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 4.7 years ago by
Rory Stark
★ 5.1k • 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
★ 5.1k • 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
★ 5.1k • written 5.2 years ago by
paz2005
• 0
0
votes
2
replies
759
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 4.3 years ago by
Gordon Smyth
50k • written 4.4 years ago by
corinne_hutfilz
• 0
0
votes
1
reply
661
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 12 months ago by
James W. MacDonald
65k • written 12 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
545
views
DiffBind t-statistic values
r
DiffBind
ATAC
updated 4.1 years ago by
Rory Stark
★ 5.1k • written 4.1 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
★ 5.1k • written 5.1 years ago by
pgontarz
▴ 10
0
votes
1
reply
640
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 14 months ago by
Rory Stark
★ 5.1k • 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
★ 5.1k • written 7.1 years ago by
BioinfGuru
▴ 20
16 results • Page
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Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
Le
• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Votes
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
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Peter Hickey
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