Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
atac-seq
•
reset
0
votes
9
replies
2.1k
views
No peak corresponding to the nucleosome-free regions is observed in Fragment size distribution of ATAC-seq
ATACseqQC
Fragmentsizedistribution
ATAC-seq
2.1 years ago
Xiaojie Cheng
• 0
3
votes
5
replies
1.6k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw
ATAC-seq
Tn5 insertions
updated 2.6 years ago by
Antonio Ahn
▴ 10 • written 2.6 years ago by
alexandre.blais
▴ 50
0
votes
5
replies
964
views
ATACSeqQC - error when splitting files using mm10
atacseqqc
atac-seq
R
bioconductor
rsamtools
updated 3.0 years ago by
Kevin Blighe
3.8k • written 3.0 years ago by
rita.monteiro
• 0
2
votes
8
replies
915
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma
edger
atac
atac-seq
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
pgugger
▴ 70
0
votes
0
replies
647
views
Job:
Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq
DNA-seq
ATAC-seq
proteomics
microbiome
Job
3.4 years ago
lhuang7
▴ 50
0
votes
0
replies
1.2k
views
Job:
Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing
RNA-Seq
ChIP-Seq
ATAC-Seq
Job
3.9 years ago • updated 3.8 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
821
views
Conditional Quantile Normalization (cqn) error
cqn
normalization
conditionalquantilenormalization
atac-seq
updated 3.9 years ago by
Kasper Daniel Hansen
6.5k • written 3.9 years ago by
Eric.Martin
• 0
1
vote
11
replies
1.5k
views
ATAC-QC shiftGAlignmentsList function
ATAC-seq
ATACseqQC
updated 3.9 years ago by
Julie Zhu
★ 4.3k • written 3.9 years ago by
Shuang He
• 0
0
votes
1
reply
625
views
ATAC-QC fragSizeDist function
ATAC-seq
ATACseqQC
updated 3.9 years ago by
Julie Zhu
★ 4.3k • written 3.9 years ago by
Shuang He
• 0
0
votes
6
replies
1.5k
views
atacseqQC error while splittin the bamfile
ATACseqQC
ATAC-seq
error
split bam file
updated 4.1 years ago by
contact
• 0 • written 4.1 years ago by
theodore.georgomanolis
• 0
0
votes
4
replies
1.4k
views
How to produce the fraction of reads in peaks (FRiP) using DiffBind
DiffBind
FRiP
ATAC-Seq
dba.show
dba.count
updated 4.2 years ago by
Rory Stark
★ 4.9k • written 4.2 years ago by
Gary
▴ 20
0
votes
0
replies
536
views
Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC
ATAC-Seq
Library complexity
estimateLibComplexity
4.2 years ago
Gary
▴ 20
2
votes
5
replies
1.1k
views
The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC
bamQC
ATAC-Seq
totalQNAMEs
MAPQ
updated 4.3 years ago by
Julie Zhu
★ 4.3k • written 4.3 years ago by
Gary
▴ 20
11
votes
21
replies
3.8k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC
ATAC-Seq
quality analysis
fragment size distribution
library complexity
updated 4.3 years ago by
Julie Zhu
★ 4.3k • written 4.3 years ago by
Gary
▴ 20
0
votes
4
replies
1.3k
views
ATAC-Seq peaks quality control with ChIPQC package, but getting error
ATAC-Seq
ChIPQC
updated 4.3 years ago by
James W. MacDonald
63k • written 4.3 years ago by
Subinoy Biswas
▴ 10
0
votes
1
reply
793
views
Use DiffBind to find differential peaks among multiple cell types
diffbind
atac-seq
differential analysis
deseq2
updated 4.6 years ago by
Rory Stark
★ 4.9k • written 4.6 years ago by
duvaller
• 0
3
votes
3
replies
1.0k
views
Differential analysis of multiple samples with different time points
diffbind
R
atac-seq
updated 4.6 years ago by
Rory Stark
★ 4.9k • written 4.6 years ago by
Firas
• 0
2
votes
2
replies
929
views
CQN and EdgeR Library Size for Normalization
CQN
atac-seq
normalization
edgeR
5.1 years ago
shankasal
• 0
6
votes
9
replies
3.9k
views
Filtering for ATAC-seq
atac-seq
CQN
edger
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
shankasal
• 0
0
votes
7
replies
1.6k
views
ATACseqQC memory overflow issue
atac-seq
software error
atacseqqc
updated 5.3 years ago by
Haibo.Liu
• 0 • written 5.3 years ago by
José Luis Lavín
▴ 10
4
votes
6
replies
1.1k
views
DESeq2 design and stats question
deseq2
differential binding analysis
deseq
atac-seq
updated 5.3 years ago by
Michael Love
40k • written 5.3 years ago by
rbronste
▴ 60
0
votes
0
replies
1.3k
views
ATAC-seq: Sample size when pooling sample reads to call peaks
atac-seq
sample size
Peak
Normalize
5.4 years ago
jaime.alvarez.benayas
• 0
4
votes
3
replies
937
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2
atac-seq
chipseq
differential binding analysis
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
rbronste
▴ 60
0
votes
0
replies
861
views
Job:
Bioinformatics Analyst II/III - Banchereau Lab @ The Jackson Laboratory
rnaseq
atac-seq
iso-seq
chipseq
Job
5.5 years ago
tyler.chukwu
• 0
0
votes
6
replies
1.5k
views
Warnings when update DiffBind and running errors
diffbind
atac-seq
dba.count
updated 5.5 years ago by
Rory Stark
★ 4.9k • written 5.5 years ago by
zhaolin20042008
• 0
0
votes
1
reply
4.5k
views
Calling differential peaks from ATAC-seq data using DEseq2
deseq2
atac-seq
updated 5.5 years ago by
Rory Stark
★ 4.9k • written 5.5 years ago by
zhongjixx
• 0
4
votes
3
replies
4.3k
views
Rsubread counting peaks ATACseq
Rsubread
atac-seq
narrowpeaks
featurecounts
updated 5.5 years ago by
Wei Shi
★ 3.5k • written 5.5 years ago by
j.bergenstrahle
▴ 80
1
vote
4
replies
1.5k
views
DiffBind error with dba.count after update
diffbind
read counting
warning message
chromatin
atac-seq
updated 5.6 years ago by
Gord Brown
▴ 650 • written 5.6 years ago by
tgjohnst
• 0
3
votes
9
replies
1.9k
views
Error When using dba.count() in DiffBind
dba.count
atac-seq
diffbind
updated 5.6 years ago by
Gord Brown
▴ 650 • written 5.6 years ago by
ew152
• 0
0
votes
1
reply
740
views
Error with dba.count function code
diffbind
dba.count
atac-seq
updated 5.6 years ago by
Gord Brown
▴ 650 • written 5.6 years ago by
VCLRAC001
• 0
0
votes
1
reply
1.4k
views
Homer getDiffExpression.pl issue
homer
atac-seq
updated 5.9 years ago by
Maciej Jończyk
• 0 • written 5.9 years ago by
niu.shengyong
• 0
0
votes
11
replies
1.5k
views
DiffBind: failed to run dba.count in SSH
SSH
atac-seq
updated 6.1 years ago by
Gord Brown
▴ 650 • written 6.1 years ago by
zhaolin20042008
• 0
1
vote
7
replies
2.9k
views
DiffBind R package issue
diffbind
atac-seq
updated 6.1 years ago by
Rory Stark
★ 4.9k • written 6.1 years ago by
niu.shengyong
• 0
0
votes
6
replies
2.1k
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
6.1 years ago
zhaolin20042008
• 0
1
vote
1
reply
1.1k
views
DiffBind: How could I debug estimateDispersionsFit (required by DBA_DESEQ2)
atac-seq
diffbind
6.1 years ago
zhaolin20042008
• 0
1
vote
7
replies
2.3k
views
loading dba.plotVolcano in DiffBind
diffbind
chipseq
atac-seq
rory stark
updated 6.2 years ago by
Rory Stark
★ 4.9k • written 6.2 years ago by
andrew.gehrke
• 0
0
votes
0
replies
897
views
Centipede foot printing export
footprinting
centipede
atac-seq
dnaseq
6.2 years ago
rbronste
▴ 60
2
votes
3
replies
8.2k
views
DiffBind for ATAC-seq
atac-seq
diffbind
macs2
macs
peak finding
updated 6.2 years ago by
BioinfGuru
▴ 20 • written 6.8 years ago by
igor
▴ 40
3
votes
4
replies
2.3k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 6.3 years ago by
Michael Love
40k • written 6.3 years ago by
g.atla
▴ 10
1
vote
4
replies
1.8k
views
DiffBind for open chromatin mapping
diffbind
dnaseseq
atac-seq
6.4 years ago
rbronste
▴ 60
0
votes
3
replies
2.3k
views
DiffBind Normalization by bFullLibrarySize
atac-seq
updated 7.2 years ago by
Rory Stark
★ 4.9k • written 7.2 years ago by
simonjean434
▴ 10
0
votes
0
replies
1.6k
views
Job:
Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq
atac-seq
gro-seq
bsseq
rnaseq
Job
7.6 years ago
Jaritz,Markus
▴ 20
42 results • Page
1 of 1
Recent ...
Replies
Answer: Extract Limma Adjusted Values for Plotting
by
James W. MacDonald
63k
You should use `removeBatchEffect` for that.
Comment: Interpret plot from DiffBind
by
Chris
• 0
Thank you for the explanation! The purple (**gain**) in the control in the right bottom corner but on the y axis is labeled **loss** which …
Comment: Use with_go along with other filters in getBM function
by
RuBBiT0
▴ 10
Thank you! I think that makes much sense to me.
Comment: Interpret plot from DiffBind
by
Rory Stark
★ 4.9k
Not necessarily. It look to me like there is reconfiguring going on, with some chromatin that was open in the control becoming closed (the …
Comment: Interpret plot from DiffBind
by
Chris
• 0
Thanks Rory! So that means the diseased sample has chromatin more open then the control one, is that correct?
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
Awards
• All
Popular Question
to
Martin Morgan
25k
Teacher
to
deeenes
▴ 30
Popular Question
to
Hervé Pagès
16k
Popular Question
to
Gordon Smyth
47k
Teacher
to
James W. MacDonald
63k
Locations
• All
United States,
2 minutes ago
United States,
5 minutes ago
United States,
6 minutes ago
Germany,
9 minutes ago
United States,
17 minutes ago
Traffic: 378 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6