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Atac
•
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0
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0
replies
68
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
10 days ago
Raghad
• 0
0
votes
1
reply
726
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 14 months ago by
James W. MacDonald
66k • written 14 months ago by
Cynthia
• 0
0
votes
1
reply
678
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 15 months ago by
Rory Stark
★ 5.2k • written 16 months ago by
Hadar
• 0
1
vote
3
replies
1.2k
views
DiffBind: reverse absolute fold change in dba.report ie. abs(rep$Fold)
diffbind
atac
updated 4.0 years ago by
Rory Stark
★ 5.2k • written 4.0 years ago by
lindsaynhayes
• 0
1
vote
1
reply
561
views
DiffBind t-statistic values
r
DiffBind
ATAC
updated 4.2 years ago by
Rory Stark
★ 5.2k • written 4.2 years ago by
lindsaynhayes
• 0
2
votes
8
replies
1.5k
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma
edger
atac
atac-seq
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
pgugger
▴ 70
0
votes
2
replies
786
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
corinne_hutfilz
• 0
0
votes
3
replies
965
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 4.8 years ago by
Rory Stark
★ 5.2k • written 4.8 years ago by
rm1238
• 0
0
votes
7
replies
1.8k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 5.0 years ago by
Steve Lianoglou
★ 13k • written 5.0 years ago by
mbasam
• 0
1
vote
1
reply
3.0k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.1 years ago by
Wei Shi
★ 3.6k • written 5.1 years ago by
aurel.nagy
▴ 10
2
votes
1
reply
1.4k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 5.2 years ago by
Rory Stark
★ 5.2k • written 5.2 years ago by
pgontarz
▴ 10
2
votes
2
replies
2.2k
views
DiffBind for ATAC-seq -- bFullLibrarySize parameter
diffbind
atac
updated 5.3 years ago by
Rory Stark
★ 5.2k • written 5.3 years ago by
paz2005
• 0
6
votes
16
replies
5.0k
views
DiffBind Batch Effect
diffbind
atac
7.0 years ago
niu.shengyong
▴ 10
5
votes
7
replies
4.6k
views
Differential binding of ATAC-seq data with no replicates
ATAC
differential binding analysis
no replicates
DEseq2
chromatin
7.2 years ago
BioinfGuru
▴ 30
0
votes
1
reply
1.4k
views
Using Diffbind on ATAC data - adapter offset issue
Diffbind
Atac
adapters
updated 7.2 years ago by
Rory Stark
★ 5.2k • written 7.2 years ago by
BioinfGuru
▴ 30
3
votes
4
replies
2.8k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 7.3 years ago by
Michael Love
42k • written 7.3 years ago by
g.atla
▴ 10
8
votes
9
replies
6.2k
views
ChIPseq-style peak calling for paired-end sequencing?
Chipseq
DNAseq
ATAC
bayespeak
narrowpeaks
updated 9.0 years ago by
Gordon Smyth
50k • written 9.0 years ago by
samuel collombet
▴ 140
17 results • Page
1 of 1
Recent ...
Replies
Comment: How to compare subset of samples from VCF files
by
Gordon Smyth
50k
Welcome to Bioconductor support. Did you know that you can delete your old postings if they haven't received an answer yet? Instead of ap…
Comment: How to compare subset of samples from VCF files
by
Marco
• 0
Here's the vcf file as code block ``` ##fileformat=VCFv4.2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth"> ##FOR…
Comment: Gviz and custom database
by
James W. MacDonald
66k
The vignette for `Gviz` says you can use a `DNAStringSet`, generated using `Biostrings`. Have you tried that?
Comment: Gviz and custom database
by
luigi.faino
• 0
Dear, this is not what I need. I need to transform a fasta sequence in a genome track usable in Gviz. L
Answer: Gviz and custom database
by
James W. MacDonald
66k
https://bioconductor.org/packages/release/bioc/vignettes/txdbmaker/inst/doc/txdbmaker.html
Votes
Answer: makeExampleDESeqDataSet using pilot data
Answer: Checking/updating package versions
Answer: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
convert data frame of Entrez IDs to Gene Symbols
Answer: LRT, pairwise comparisons and p-value adjustment
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Gordon Smyth
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Marco Blanchette
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Fred Hutch (Recruiting)
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James W. MacDonald
66k
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Levi Waldron
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