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Showing :
atac-seq
•
reset
0
votes
9
replies
908
views
No peak corresponding to the nucleosome-free regions is observed in Fragment size distribution of ATAC-seq
ATACseqQC
Fragmentsizedistribution
ATAC-seq
12 months ago
Xiaojie Cheng
• 0
3
votes
5
replies
883
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw
ATAC-seq
Tn5 insertions
updated 18 months ago by
Antonio Ahn
▴ 10 • written 19 months ago by
alexandre.blais
▴ 50
0
votes
5
replies
559
views
ATACSeqQC - error when splitting files using mm10
atacseqqc
atac-seq
R
bioconductor
rsamtools
updated 24 months ago by
Kevin Blighe
3.5k • written 24 months ago by
rita.monteiro
• 0
2
votes
8
replies
562
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma
edger
atac
atac-seq
updated 2.2 years ago by
Aaron Lun
★ 27k • written 2.2 years ago by
pgugger
▴ 60
0
votes
0
replies
401
views
Job:
Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq
DNA-seq
ATAC-seq
proteomics
microbiome
Job
2.4 years ago
lhuang7
▴ 50
0
votes
0
replies
998
views
Job:
Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing
RNA-Seq
ChIP-Seq
ATAC-Seq
Job
2.9 years ago • updated 2.7 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
627
views
Conditional Quantile Normalization (cqn) error
cqn
normalization
conditionalquantilenormalization
atac-seq
updated 2.8 years ago by
Kasper Daniel Hansen
6.5k • written 2.8 years ago by
Eric.Martin
• 0
1
vote
11
replies
982
views
ATAC-QC shiftGAlignmentsList function
ATAC-seq
ATACseqQC
updated 2.8 years ago by
Julie Zhu
★ 4.3k • written 2.8 years ago by
Shuang He
• 0
0
votes
1
reply
415
views
ATAC-QC fragSizeDist function
ATAC-seq
ATACseqQC
updated 2.8 years ago by
Julie Zhu
★ 4.3k • written 2.8 years ago by
Shuang He
• 0
0
votes
6
replies
1.1k
views
atacseqQC error while splittin the bamfile
ATACseqQC
ATAC-seq
error
split bam file
updated 3.0 years ago by
contact
• 0 • written 3.0 years ago by
theodore.georgomanolis
• 0
0
votes
4
replies
805
views
How to produce the fraction of reads in peaks (FRiP) using DiffBind
DiffBind
FRiP
ATAC-Seq
dba.show
dba.count
updated 3.2 years ago by
Rory Stark
★ 4.4k • written 3.2 years ago by
Gary
▴ 20
0
votes
0
replies
393
views
Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC
ATAC-Seq
Library complexity
estimateLibComplexity
3.2 years ago
Gary
▴ 20
2
votes
5
replies
731
views
The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC
bamQC
ATAC-Seq
totalQNAMEs
MAPQ
updated 3.2 years ago by
Julie Zhu
★ 4.3k • written 3.2 years ago by
Gary
▴ 20
11
votes
21
replies
2.9k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC
ATAC-Seq
quality analysis
fragment size distribution
library complexity
updated 3.3 years ago by
Julie Zhu
★ 4.3k • written 3.3 years ago by
Gary
▴ 20
0
votes
4
replies
1.0k
views
ATAC-Seq peaks quality control with ChIPQC package, but getting error
ATAC-Seq
ChIPQC
updated 3.3 years ago by
James W. MacDonald
59k • written 3.3 years ago by
Subinoy Biswas
▴ 10
0
votes
1
reply
557
views
Use DiffBind to find differential peaks among multiple cell types
diffbind
atac-seq
differential analysis
deseq2
updated 3.5 years ago by
Rory Stark
★ 4.4k • written 3.6 years ago by
duvaller
• 0
3
votes
3
replies
768
views
Differential analysis of multiple samples with different time points
diffbind
R
atac-seq
updated 3.6 years ago by
Rory Stark
★ 4.4k • written 3.6 years ago by
Firas
• 0
2
votes
2
replies
659
views
CQN and EdgeR Library Size for Normalization
CQN
atac-seq
normalization
edgeR
4.0 years ago
shankasal
• 0
6
votes
9
replies
3.0k
views
Filtering for ATAC-seq
atac-seq
CQN
edger
updated 4.0 years ago by
Aaron Lun
★ 27k • written 4.0 years ago by
shankasal
• 0
0
votes
7
replies
1.2k
views
ATACseqQC memory overflow issue
atac-seq
software error
atacseqqc
updated 4.2 years ago by
Haibo.Liu
• 0 • written 4.3 years ago by
José Luis Lavín
▴ 10
4
votes
6
replies
790
views
DESeq2 design and stats question
deseq2
differential binding analysis
deseq
atac-seq
updated 4.3 years ago by
Michael Love
36k • written 4.3 years ago by
rbronste
▴ 60
0
votes
0
replies
968
views
ATAC-seq: Sample size when pooling sample reads to call peaks
atac-seq
sample size
Peak
Normalize
4.3 years ago
jaime.alvarez.benayas
• 0
4
votes
3
replies
704
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2
atac-seq
chipseq
differential binding analysis
updated 4.4 years ago by
Aaron Lun
★ 27k • written 4.4 years ago by
rbronste
▴ 60
0
votes
0
replies
668
views
Job:
Bioinformatics Analyst II/III - Banchereau Lab @ The Jackson Laboratory
rnaseq
atac-seq
iso-seq
chipseq
Job
4.4 years ago
tyler.chukwu
• 0
0
votes
6
replies
1.2k
views
Warnings when update DiffBind and running errors
diffbind
atac-seq
dba.count
updated 4.5 years ago by
Rory Stark
★ 4.4k • written 4.5 years ago by
zhaolin20042008
• 0
0
votes
1
reply
4.0k
views
Calling differential peaks from ATAC-seq data using DEseq2
deseq2
atac-seq
updated 4.5 years ago by
Rory Stark
★ 4.4k • written 4.5 years ago by
zhongjixx
• 0
4
votes
3
replies
3.2k
views
Rsubread counting peaks ATACseq
Rsubread
atac-seq
narrowpeaks
featurecounts
updated 4.5 years ago by
Wei Shi
★ 3.4k • written 4.5 years ago by
j.bergenstrahle
▴ 80
1
vote
4
replies
1.0k
views
DiffBind error with dba.count after update
diffbind
read counting
warning message
chromatin
atac-seq
updated 4.5 years ago by
Gord Brown
▴ 640 • written 4.5 years ago by
tgjohnst
• 0
3
votes
9
replies
1.4k
views
Error When using dba.count() in DiffBind
dba.count
atac-seq
diffbind
updated 4.5 years ago by
Gord Brown
▴ 640 • written 4.5 years ago by
ew152
• 0
0
votes
1
reply
535
views
Error with dba.count function code
diffbind
dba.count
atac-seq
updated 4.6 years ago by
Gord Brown
▴ 640 • written 4.6 years ago by
VCLRAC001
• 0
0
votes
1
reply
1.1k
views
Homer getDiffExpression.pl issue
homer
atac-seq
updated 4.8 years ago by
Maciej Jończyk
• 0 • written 4.9 years ago by
niu.shengyong
• 0
0
votes
11
replies
1.1k
views
DiffBind: failed to run dba.count in SSH
SSH
atac-seq
updated 5.0 years ago by
Gord Brown
▴ 640 • written 5.0 years ago by
zhaolin20042008
• 0
1
vote
7
replies
2.3k
views
DiffBind R package issue
diffbind
atac-seq
updated 5.1 years ago by
Rory Stark
★ 4.4k • written 5.1 years ago by
niu.shengyong
• 0
0
votes
6
replies
1.5k
views
Error in lfproc(x, y, weights = weights, cens = cens,... : newsplit: out of vertex space in dba.analyze(diff_contrast, method=DBA_DESEQ2)
atac-seq
diffbind
5.1 years ago
zhaolin20042008
• 0
1
vote
1
reply
892
views
DiffBind: How could I debug estimateDispersionsFit (required by DBA_DESEQ2)
atac-seq
diffbind
5.1 years ago
zhaolin20042008
• 0
1
vote
7
replies
2.0k
views
loading dba.plotVolcano in DiffBind
diffbind
chipseq
atac-seq
rory stark
updated 5.1 years ago by
Rory Stark
★ 4.4k • written 5.1 years ago by
andrew.gehrke
• 0
0
votes
0
replies
739
views
Centipede foot printing export
footprinting
centipede
atac-seq
dnaseq
5.1 years ago
rbronste
▴ 60
2
votes
3
replies
7.2k
views
DiffBind for ATAC-seq
atac-seq
diffbind
macs2
macs
peak finding
updated 5.2 years ago by
YaGalbi
▴ 20 • written 5.7 years ago by
igor
▴ 40
3
votes
4
replies
1.9k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 5.2 years ago by
Michael Love
36k • written 5.2 years ago by
g.atla
▴ 10
1
vote
4
replies
1.6k
views
DiffBind for open chromatin mapping
diffbind
dnaseseq
atac-seq
5.3 years ago
rbronste
▴ 60
0
votes
3
replies
2.1k
views
DiffBind Normalization by bFullLibrarySize
atac-seq
updated 6.2 years ago by
Rory Stark
★ 4.4k • written 6.2 years ago by
simonjean434
▴ 10
0
votes
0
replies
1.4k
views
Job:
Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq
atac-seq
gro-seq
bsseq
rnaseq
Job
6.5 years ago
Jaritz,Markus
▴ 20
42 results • Page
1 of 1
Recent ...
Replies
Comment: Quantile Normalization after rma or not?
by
Yang Shi
• 0
Thanks you so much sir! But I'm still confused with the boxplot showing here. Why oligo::rma could not get the plot like limma::normalizeBe…
Answer: how to understand cpm=1 and how filterByExpr works?
by
gowthamee
• 0
I found the following two articles very helpful in explaining the functions "cpm" and "filterByExpr" Article#1: From reads to genes to pat…
Comment: different results in DESeq2 when comparing groups in two ways
by
zohreh.fazelan
• 0
Thank you for your response. But I have few comparisons in which there are more significantly expressed genes in the socond way compared to…
Comment: lmFit, continuous exposure, adjustment covariates
by
Gordon Smyth
45k
Your code `t(dat[43:ncol(dat)]` is not even syntactically correct. It could not possibly run in R. You need to create an expression matrix…
Comment: Handling of missing values in limma
by
Gordon Smyth
45k
limma uses all the observations. There's nothing complicated about it. limma does not remove any persons from the analysis. I did not tel…
Votes
A: redundant probe sets in Affymetrix HG-U219
Answer: Quantile Normalization after rma or not?
Answer: Quantile Normalization after rma or not?
Answer: Using featureCounts and downloading Rsubread
Answer: different results in DESeq2 when comparing groups in two ways
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