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Atac
•
reset
0
votes
0
replies
447
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
7 months ago
Raghad
• 0
0
votes
1
reply
1.0k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 21 months ago by
James W. MacDonald
67k • written 21 months ago by
Cynthia
• 0
0
votes
1
reply
864
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 22 months ago by
Rory Stark
★ 5.2k • written 22 months ago by
Hadar
• 0
1
vote
3
replies
1.5k
views
DiffBind: reverse absolute fold change in dba.report ie. abs(rep$Fold)
diffbind
atac
updated 4.6 years ago by
Rory Stark
★ 5.2k • written 4.6 years ago by
lindsaynhayes
• 0
1
vote
1
reply
685
views
DiffBind t-statistic values
r
DiffBind
ATAC
updated 4.8 years ago by
Rory Stark
★ 5.2k • written 4.8 years ago by
lindsaynhayes
• 0
2
votes
8
replies
1.8k
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma
edger
atac
atac-seq
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
pgugger
▴ 70
0
votes
2
replies
927
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 5.0 years ago by
Gordon Smyth
52k • written 5.0 years ago by
corinne_hutfilz
• 0
0
votes
3
replies
1.1k
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 5.4 years ago by
Rory Stark
★ 5.2k • written 5.4 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 5.5 years ago by
Steve Lianoglou
★ 13k • written 5.5 years ago by
mbasam
• 0
1
vote
1
reply
3.5k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.7 years ago by
Wei Shi
★ 3.6k • written 5.7 years ago by
aurel.nagy
▴ 10
2
votes
1
reply
1.6k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 5.7 years ago by
Rory Stark
★ 5.2k • written 5.8 years ago by
pgontarz
▴ 10
2
votes
2
replies
2.5k
views
DiffBind for ATAC-seq -- bFullLibrarySize parameter
diffbind
atac
updated 5.8 years ago by
Rory Stark
★ 5.2k • written 5.8 years ago by
paz2005
• 0
6
votes
16
replies
5.9k
views
DiffBind Batch Effect
diffbind
atac
7.6 years ago • updated 7.5 years ago
niu.shengyong
▴ 10
5
votes
7
replies
5.0k
views
Differential binding of ATAC-seq data with no replicates
ATAC
differential binding analysis
no replicates
DEseq2
chromatin
7.8 years ago
BioinfGuru
▴ 70
0
votes
1
reply
1.5k
views
Using Diffbind on ATAC data - adapter offset issue
Diffbind
Atac
adapters
updated 7.8 years ago by
Rory Stark
★ 5.2k • written 7.8 years ago by
BioinfGuru
▴ 70
3
votes
4
replies
3.2k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
g.atla
▴ 10
8
votes
9
replies
6.6k
views
ChIPseq-style peak calling for paired-end sequencing?
Chipseq
DNAseq
ATAC
bayespeak
narrowpeaks
updated 9.6 years ago by
Gordon Smyth
52k • written 9.6 years ago by
samuel collombet
▴ 140
17 results • Page
1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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Ali Barry
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gabriel.hoffman
▴ 170
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to
Jenny Drnevich
★ 2.0k
Popular Question
to
martin.grigorov
▴ 10
Scholar
to
James W. MacDonald
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