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ATAC
•
reset
0
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0
replies
553
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
8 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 22 months ago by
James W. MacDonald
68k • written 22 months ago by
Cynthia
• 0
0
votes
1
reply
907
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 24 months 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 4.7 years ago by
Rory Stark
★ 5.2k • written 4.7 years ago by
lindsaynhayes
• 0
1
vote
1
reply
705
views
DiffBind t-statistic values
r
DiffBind
ATAC
updated 4.9 years ago by
Rory Stark
★ 5.2k • written 4.9 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
956
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
2.1k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 5.6 years ago by
Steve Lianoglou
★ 13k • written 5.6 years ago by
mbasam
• 0
1
vote
1
reply
3.6k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.8 years ago by
Wei Shi
★ 3.6k • written 5.8 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
6.7k
views
ChIPseq-style peak calling for paired-end sequencing?
Chipseq
DNAseq
ATAC
bayespeak
narrowpeaks
updated 9.7 years ago by
Gordon Smyth
52k • written 9.7 years ago by
samuel collombet
▴ 140
17 results • Page
1 of 1
Recent ...
Replies
Comment: WGCNA coupled with differential expression analysis: question about baseline mod
by
hetaf16210
• 0
@[slope][1] If feasible, consider conducting both analyses. Start with a pooled analysis to identify broad patterns, then conduct separate …
Comment: DESeq2 adujsted p-value cutoff seemingly not working
by
980linnet
• 0
Stuck on DESeq2 with alpha=.05 for padj cutoff. Can't seem to get the differential expression analysis to stick the landing - it's like try…
Comment: internal error in trio library when trying to use lfmm() in LEA package
by
PW
• 0
>ERROR: unable to open file D://anole_geno.snmf/K1/run1/anole_geno_r1.1.Q. Please, check that the name of the file you provided is correct.…
Comment: DESeq2 adujsted p-value cutoff seemingly not working
by
Guilherme
• 0
Thank you for your answer So the proper way to conduct the analysis is to put the filters in the results() function and later filter the da…
Comment: DiffBind - observation that the default union overlap is actually a gap of 1 bp
by
Ian D.
▴ 70
Please can you comment on this @rory.
Votes
A: how to extract Granges not overlapping with other ganges?
DESeq2 1.20.0 lfcshrink function
A: LIMMA on RT-PCR data
Answer: Efficiently working with HDF5-backed SingleCellExperiments
Efficiently working with HDF5-backed SingleCellExperiments
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ramiro.barrantes
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Vincent J. Carey, Jr.
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