Showing : atac-seq • reset
0
votes
9
replies
326
views
No peak corresponding to the nucleosome-free regions is observed in Fragment size distribution of ATAC-seq
ATACseqQC Fragmentsizedistribution ATAC-seq
7 weeks ago • updated 5 weeks ago Xiaojie Cheng • 0
3
votes
5
replies
363
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 7 months ago by ▴ 10 • written 8 months ago by ▴ 30
0
votes
5
replies
295
views
ATACSeqQC - error when splitting files using mm10
atacseqqc atac-seq R bioconductor rsamtools
updated 13 months ago by 3.1k • written 13 months ago by • 0
2
votes
8
replies
306
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma edger atac atac-seq
updated 15 months ago by ★ 26k • written 15 months ago by ▴ 50
0
votes
0
replies
200
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
17 months ago lhuang7 ▴ 50
0
votes
0
replies
832
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
23 months ago • updated 22 months ago Julie Zhu ★ 4.3k
0
votes
1
reply
486
views
Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 23 months ago by 6.5k • written 23 months ago by • 0
1
vote
11
replies
619
views
ATAC-QC shiftGAlignmentsList function
ATAC-seq ATACseqQC
updated 23 months ago by ★ 4.3k • written 23 months ago by • 0
0
votes
1
reply
219
views
ATAC-QC fragSizeDist function
ATAC-seq ATACseqQC
updated 23 months ago by ★ 4.3k • written 23 months ago by • 0
0
votes
6
replies
726
views
atacseqQC error while splittin the bamfile
ATACseqQC ATAC-seq error split bam file
updated 2.1 years ago by • 0 • written 2.1 years ago by • 0
0
votes
4
replies
500
views
How to produce the fraction of reads in peaks (FRiP) using DiffBind
DiffBind FRiP ATAC-Seq dba.show dba.count
updated 2.2 years ago by ★ 3.9k • written 2.2 years ago by ▴ 20
0
votes
0
replies
275
views
Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC ATAC-Seq Library complexity estimateLibComplexity
2.2 years ago Gary ▴ 20
2
votes
5
replies
475
views
The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC bamQC ATAC-Seq totalQNAMEs MAPQ
updated 2.3 years ago by ★ 4.3k • written 2.3 years ago by ▴ 20
11
votes
21
replies
2.2k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity
updated 2.3 years ago by ★ 4.3k • written 2.3 years ago by ▴ 20
0
votes
4
replies
745
views
ATAC-Seq peaks quality control with ChIPQC package, but getting error
ATAC-Seq ChIPQC
updated 2.4 years ago by 57k • written 2.4 years ago by ▴ 10
0
votes
1
reply
400
views
Use DiffBind to find differential peaks among multiple cell types
diffbind atac-seq differential analysis deseq2
updated 2.6 years ago by ★ 3.9k • written 2.6 years ago by • 0
3
votes
3
replies
521
views
Differential analysis of multiple samples with different time points
diffbind R atac-seq
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
2
votes
2
replies
497
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
3.1 years ago shankasal • 0
6
votes
9
replies
2.5k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 3.1 years ago by ★ 26k • written 3.1 years ago by • 0
0
votes
7
replies
864
views
ATACseqQC memory overflow issue
atac-seq software error atacseqqc
updated 3.3 years ago by • 0 • written 3.3 years ago by ▴ 10
4
votes
6
replies
624
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 3.4 years ago by 33k • written 3.4 years ago by ▴ 60
0
votes
0
replies
740
views
ATAC-seq: Sample size when pooling sample reads to call peaks
atac-seq sample size Peak Normalize
3.4 years ago jaime.alvarez.benayas • 0
4
votes
3
replies
584
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 3.5 years ago by ★ 26k • written 3.5 years ago by ▴ 60
0
votes
0
replies
573
views
Job: Bioinformatics Analyst II/III - Banchereau Lab @ The Jackson Laboratory
rnaseq atac-seq iso-seq chipseq Job
3.5 years ago tyler.chukwu • 0
0
votes
6
replies
851
views
Warnings when update DiffBind and running errors
diffbind atac-seq dba.count
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
0
votes
1
reply
3.5k
views
Calling differential peaks from ATAC-seq data using DEseq2
deseq2 atac-seq
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
4
votes
3
replies
2.5k
views
Rsubread counting peaks ATACseq
Rsubread atac-seq narrowpeaks featurecounts
updated 3.6 years ago by ★ 3.3k • written 3.6 years ago by ▴ 80
1
vote
4
replies
808
views
DiffBind error with dba.count after update
diffbind read counting warning message chromatin atac-seq
updated 3.6 years ago by ▴ 630 • written 3.6 years ago by • 0
3
votes
9
replies
987
views
Error When using dba.count() in DiffBind
dba.count atac-seq diffbind
updated 3.6 years ago by ▴ 630 • written 3.6 years ago by • 0
0
votes
1
reply
423
views
Error with dba.count function code
diffbind dba.count atac-seq
updated 3.6 years ago by ▴ 630 • written 3.6 years ago by • 0
0
votes
1
reply
823
views
Homer getDiffExpression.pl issue
homer atac-seq
updated 3.9 years ago by • 0 • written 3.9 years ago by • 0
0
votes
11
replies
918
views
DiffBind: failed to run dba.count in SSH
SSH atac-seq
updated 4.1 years ago by ▴ 630 • written 4.1 years ago by • 0
1
vote
7
replies
2.0k
views
DiffBind R package issue
diffbind atac-seq
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by • 0
0
votes
6
replies
1.2k
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
4.2 years ago zhaolin20042008 • 0
1
vote
1
reply
742
views
DiffBind: How could I debug estimateDispersionsFit (required by DBA_DESEQ2)
atac-seq diffbind
4.2 years ago zhaolin20042008 • 0
1
vote
7
replies
1.8k
views
loading dba.plotVolcano in DiffBind
diffbind chipseq atac-seq rory stark
updated 4.2 years ago by ★ 3.9k • written 4.2 years ago by • 0
0
votes
0
replies
620
views
Centipede foot printing export
footprinting centipede atac-seq dnaseq
4.2 years ago rbronste ▴ 60
2
votes
3
replies
6.6k
views
DiffBind for ATAC-seq
atac-seq diffbind macs2 macs peak finding
updated 4.2 years ago by ▴ 20 • written 4.8 years ago by ▴ 40
3
votes
4
replies
1.4k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 4.3 years ago by 33k • written 4.3 years ago by ▴ 10
1
vote
4
replies
1.5k
views
DiffBind for open chromatin mapping
diffbind dnaseseq atac-seq
4.4 years ago rbronste ▴ 60
0
votes
3
replies
1.8k
views
DiffBind Normalization by bFullLibrarySize
atac-seq
updated 5.3 years ago by ★ 3.9k • written 5.3 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Job: Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq atac-seq gro-seq bsseq rnaseq Job
5.6 years ago Jaritz,Markus ▴ 20
42 results • Page 1 of 1
Recent ...
Replies
Answer: Statistical Bioinformatics Laboratory Head, WEHI, Melbourne, Australia by Gordon Smyth 43k
A reminder that applications close tomorrow, at 5pm 15 June (Eastern Australian time).
Answer: No counts, just fold change data by swbarnes2 ▴ 770
> in order to connect the differentially expressed genes to pathways, > filter what is relevant and further analyse the network. I thin…
Comment: How to do annotation with Limma by James W. MacDonald 57k
I should also point out that the fid isn't really the probe ID. For this array (and IIRC all of the random-primer arrays), there really isn…
Comment: How to do annotation with Limma by James W. MacDonald 57k
The probe IDs are different from the probeset IDs, and are usually not of interest. Each probeset is made up of 4 or more probes (depending…
Comment: How to do annotation with Limma by 1gagoogag1 • 0
Thank you so much for your explanation! I have a question about how can I get the probeIDs and are they different from the probe set ID?
Votes
How to select summit size for histone ChiP-Seq in Diffbind
A: How to select summit size for histone ChiP-Seq in Diffbind
Correct use of TMM / normalization factors based on large bins
Answer: How to do annotation with Limma
Final List of Deprecated Packages for Bioc3.13
Awards • All
Popular Question to k.vitting.seerup ▴ 100
Teacher to A ▴ 40
Popular Question to Guido Hooiveld ★ 3.0k
Popular Question to Gordon Smyth 43k
Popular Question to yueli7 ▴ 10
Locations • All
United States, 7 minutes ago
WEHI, Melbourne, Australia, 29 minutes ago
Spain, 40 minutes ago
United States, 59 minutes ago
San Diego, 1 hour ago
Traffic: 320 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