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Atac
•
reset
0
votes
0
replies
1.0k
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
18 months ago
Raghad
• 0
0
votes
1
reply
1.6k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Cynthia
• 0
0
votes
1
reply
1.2k
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 2.8 years ago by
Rory Stark
★ 5.2k • written 2.8 years ago by
Hadar
• 0
1
vote
3
replies
1.8k
views
DiffBind: reverse absolute fold change in dba.report ie. abs(rep$Fold)
diffbind
atac
updated 5.5 years ago by
Rory Stark
★ 5.2k • written 5.5 years ago by
lindsaynhayes
• 0
1
vote
1
reply
861
views
DiffBind t-statistic values
r
DiffBind
ATAC
updated 5.7 years ago by
Rory Stark
★ 5.2k • written 5.7 years ago by
lindsaynhayes
• 0
2
votes
8
replies
2.4k
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma
edger
atac
atac-seq
updated 5.8 years ago by
Aaron Lun
★ 29k • written 5.8 years ago by
pgugger
▴ 70
0
votes
2
replies
1.2k
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 6.0 years ago by
Gordon Smyth
53k • written 6.0 years ago by
corinne_hutfilz
• 0
0
votes
3
replies
1.4k
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 6.3 years ago by
Rory Stark
★ 5.2k • written 6.3 years ago by
rm1238
• 0
0
votes
7
replies
2.5k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 6.4 years ago by
Steve Lianoglou
★ 13k • written 6.4 years ago by
mbasam
• 0
1
vote
1
reply
4.2k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 6.6 years ago by
Wei Shi
★ 3.6k • written 6.6 years ago by
aurel.nagy
▴ 10
2
votes
1
reply
2.0k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 6.7 years ago by
Rory Stark
★ 5.2k • written 6.7 years ago by
pgontarz
▴ 10
2
votes
2
replies
2.9k
views
DiffBind for ATAC-seq -- bFullLibrarySize parameter
diffbind
atac
updated 6.8 years ago by
Rory Stark
★ 5.2k • written 6.8 years ago by
paz2005
• 0
6
votes
16
replies
7.0k
views
DiffBind Batch Effect
diffbind
atac
8.5 years ago
niu.shengyong
▴ 10
5
votes
7
replies
5.6k
views
Differential binding of ATAC-seq data with no replicates
ATAC
differential binding analysis
no replicates
DEseq2
chromatin
8.7 years ago
BioinfGuru
▴ 70
0
votes
1
reply
1.7k
views
Using Diffbind on ATAC data - adapter offset issue
Diffbind
Atac
adapters
updated 8.7 years ago by
Rory Stark
★ 5.2k • written 8.7 years ago by
BioinfGuru
▴ 70
3
votes
4
replies
3.7k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 8.8 years ago by
Michael Love
43k • written 8.8 years ago by
g.atla
▴ 10
8
votes
9
replies
7.3k
views
ChIPseq-style peak calling for paired-end sequencing?
Chipseq
DNAseq
ATAC
bayespeak
narrowpeaks
updated 10.5 years ago by
Gordon Smyth
53k • written 10.5 years ago by
samuel collombet
▴ 140
17 results • Page
1 of 1
Recent ...
Replies
Comment: upstream git branches of bioc-release
by
TrentonCollier99
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release
by
Jeroen
▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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