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atac
•
reset
0
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704
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FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
11 months ago
Raghad
• 0
0
votes
1
reply
1.3k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
Cynthia
• 0
0
votes
1
reply
982
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 2.2 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
737
views
DiffBind t-statistic values
r
DiffBind
ATAC
updated 5.1 years ago by
Rory Stark
★ 5.2k • written 5.2 years ago by
lindsaynhayes
• 0
2
votes
8
replies
2.1k
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma
edger
atac
atac-seq
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
pgugger
▴ 70
0
votes
2
replies
999
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 5.4 years ago by
Gordon Smyth
52k • written 5.4 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
2.3k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 5.9 years ago by
Steve Lianoglou
★ 13k • written 5.9 years ago by
mbasam
• 0
1
vote
1
reply
3.9k
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
1.8k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 6.1 years ago by
Rory Stark
★ 5.2k • written 6.1 years ago by
pgontarz
▴ 10
2
votes
2
replies
2.7k
views
DiffBind for ATAC-seq -- bFullLibrarySize parameter
diffbind
atac
updated 6.2 years ago by
Rory Stark
★ 5.2k • written 6.2 years ago by
paz2005
• 0
6
votes
16
replies
6.4k
views
DiffBind Batch Effect
diffbind
atac
7.9 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
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
3.5k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 8.2 years ago by
Michael Love
43k • written 8.2 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
1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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