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atac
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FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
10 months ago
Raghad
• 0
0
votes
1
reply
1.2k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
Cynthia
• 0
0
votes
1
reply
960
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 2.1 years ago by
Rory Stark
★ 5.2k • written 2.2 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 4.9 years ago by
Rory Stark
★ 5.2k • written 4.9 years ago by
lindsaynhayes
• 0
1
vote
1
reply
726
views
DiffBind t-statistic values
r
DiffBind
ATAC
updated 5.1 years ago by
Rory Stark
★ 5.2k • written 5.1 years ago by
lindsaynhayes
• 0
2
votes
8
replies
2.0k
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma
edger
atac
atac-seq
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
pgugger
▴ 70
0
votes
2
replies
994
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 5.3 years ago by
Gordon Smyth
52k • written 5.3 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 5.7 years ago by
Rory Stark
★ 5.2k • written 5.7 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 5.8 years ago by
Steve Lianoglou
★ 13k • written 5.8 years ago by
mbasam
• 0
1
vote
1
reply
3.8k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 6.0 years ago by
Wei Shi
★ 3.6k • written 6.0 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 6.0 years ago by
Rory Stark
★ 5.2k • written 6.1 years ago by
pgontarz
▴ 10
2
votes
2
replies
2.6k
views
DiffBind for ATAC-seq -- bFullLibrarySize parameter
diffbind
atac
updated 6.1 years ago by
Rory Stark
★ 5.2k • written 6.1 years ago by
paz2005
• 0
6
votes
16
replies
6.3k
views
DiffBind Batch Effect
diffbind
atac
7.9 years ago • updated 7.8 years ago
niu.shengyong
▴ 10
5
votes
7
replies
5.3k
views
Differential binding of ATAC-seq data with no replicates
ATAC
differential binding analysis
no replicates
DEseq2
chromatin
8.1 years ago • updated 8.0 years ago
BioinfGuru
▴ 70
0
votes
1
reply
1.6k
views
Using Diffbind on ATAC data - adapter offset issue
Diffbind
Atac
adapters
updated 8.1 years ago by
Rory Stark
★ 5.2k • written 8.1 years ago by
BioinfGuru
▴ 70
3
votes
4
replies
3.4k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 8.1 years ago by
Michael Love
43k • written 8.1 years ago by
g.atla
▴ 10
8
votes
9
replies
6.9k
views
ChIPseq-style peak calling for paired-end sequencing?
Chipseq
DNAseq
ATAC
bayespeak
narrowpeaks
updated 9.9 years ago by
Gordon Smyth
52k • written 9.9 years ago by
samuel collombet
▴ 140
17 results • Page
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Answer: DESeq2 - am I extracting results incorrectly?
by
James W. MacDonald
68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
• 0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Answer: Origin of the labels for the SingleCellMultiModal dataset
by
ATpoint
★ 4.8k
If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
ATpoint
★ 4.8k
That plot looks extremely worrying. You have very unbalanced DE profiles and clearly two populations of peaks on the right. I would make su…
Answer: Having Trouble Using CNE12() and CNE21() in CNEr
by
1324087964
• 0
![enter image description here][1] [1]: /media/images/d1a91557-b19e-4fbf-b5a1-c4fd42b9
Votes
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
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