Showing : ATAC-Seq • reset
1
vote
11
replies
2.3k
views
ATAC-QC shiftGAlignmentsList function
ATAC-seq ATACseqQC
updated 4.8 years ago by ★ 4.3k • written 4.8 years ago by • 0
0
votes
9
replies
3.5k
views
No peak corresponding to the nucleosome-free regions is observed in Fragment size distribution of ATAC-seq
ATACseqQC Fragmentsizedistribution ATAC-seq
3.0 years ago Xiaojie Cheng • 0
3
votes
9
replies
2.6k
views
Error When using dba.count() in DiffBind
dba.count atac-seq diffbind
updated 6.4 years ago by ▴ 650 • written 6.5 years ago by • 0
0
votes
6
replies
2.7k
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
7.0 years ago zhaolin20042008 • 0
2
votes
3
replies
9.2k
views
DiffBind for ATAC-seq
atac-seq diffbind macs2 macs peak finding
updated 7.1 years ago by ▴ 30 • written 7.7 years ago by ▴ 40
1
vote
7
replies
3.6k
views
DiffBind R package issue
diffbind atac-seq
updated 7.0 years ago by ★ 5.2k • written 7.0 years ago by • 0
2
votes
2
replies
1.3k
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
6.0 years ago shankasal • 0
4
votes
3
replies
1.2k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 60
0
votes
7
replies
2.2k
views
ATACseqQC memory overflow issue
atac-seq software error atacseqqc
updated 6.2 years ago by • 0 • written 6.2 years ago by ▴ 10
2
votes
5
replies
1.5k
views
The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC bamQC ATAC-Seq totalQNAMEs MAPQ
updated 5.2 years ago by ★ 4.3k • written 5.2 years ago by ▴ 20
1
vote
7
replies
2.7k
views
loading dba.plotVolcano in DiffBind
diffbind chipseq atac-seq rory stark
updated 7.0 years ago by ★ 5.2k • written 7.1 years ago by • 0
0
votes
1
reply
1.1k
views
Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 4.8 years ago by ★ 6.5k • written 4.8 years ago by • 0
0
votes
3
replies
2.6k
views
DiffBind Normalization by bFullLibrarySize
atac-seq
updated 8.1 years ago by ★ 5.2k • written 8.1 years ago by ▴ 10
3
votes
4
replies
2.8k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 7.2 years ago by 41k • written 7.2 years ago by ▴ 10
0
votes
11
replies
2.0k
views
DiffBind: failed to run dba.count in SSH
SSH atac-seq
updated 7.0 years ago by ▴ 650 • written 7.0 years ago by • 0
0
votes
1
reply
1.9k
views
Homer getDiffExpression.pl issue
homer atac-seq
updated 6.8 years ago by • 0 • written 6.8 years ago by • 0
0
votes
1
reply
1.0k
views
Error with dba.count function code
diffbind dba.count atac-seq
updated 6.5 years ago by ▴ 650 • written 6.5 years ago by • 0
1
vote
4
replies
2.0k
views
DiffBind error with dba.count after update
diffbind read counting warning message chromatin atac-seq
updated 6.4 years ago by ▴ 650 • written 6.5 years ago by • 0
4
votes
3
replies
5.5k
views
Rsubread counting peaks ATACseq
Rsubread atac-seq narrowpeaks featurecounts
updated 6.4 years ago by ★ 3.6k • written 6.4 years ago by ▴ 80
0
votes
1
reply
5.3k
views
Calling differential peaks from ATAC-seq data using DEseq2
deseq2 atac-seq
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
0
votes
6
replies
2.0k
views
Warnings when update DiffBind and running errors
diffbind atac-seq dba.count
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
4
votes
6
replies
1.5k
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 6.2 years ago by 41k • written 6.2 years ago by ▴ 60
6
votes
9
replies
4.9k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
3
votes
3
replies
1.4k
views
Differential analysis of multiple samples with different time points
diffbind R atac-seq
updated 5.5 years ago by ★ 5.2k • written 5.5 years ago by • 0
0
votes
1
reply
1.1k
views
Use DiffBind to find differential peaks among multiple cell types
diffbind atac-seq differential analysis deseq2
updated 5.5 years ago by ★ 5.2k • written 5.5 years ago by • 0
11
votes
21
replies
5.0k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity
updated 5.2 years ago by ★ 4.3k • written 5.2 years ago by ▴ 20
0
votes
4
replies
2.0k
views
How to produce the fraction of reads in peaks (FRiP) using DiffBind
DiffBind FRiP ATAC-Seq dba.show dba.count
updated 5.1 years ago by ★ 5.2k • written 5.1 years ago by ▴ 20
0
votes
6
replies
1.9k
views
atacseqQC error while splittin the bamfile
ATACseqQC ATAC-seq error split bam file
updated 5.0 years ago by • 0 • written 5.0 years ago by ▴ 10
0
votes
1
reply
953
views
ATAC-QC fragSizeDist function
ATAC-seq ATACseqQC
updated 4.8 years ago by ★ 4.3k • written 4.8 years ago by • 0
2
votes
8
replies
1.4k
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma edger atac atac-seq
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 70
3
votes
5
replies
2.5k
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 3.5 years ago by ▴ 10 • written 3.5 years ago by ▴ 50
0
votes
0
replies
765
views
Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC ATAC-Seq Library complexity estimateLibComplexity
5.1 years ago Gary ▴ 20
1
vote
4
replies
2.2k
views
DiffBind for open chromatin mapping
diffbind dnaseseq atac-seq
7.3 years ago rbronste ▴ 60
0
votes
0
replies
1.6k
views
ATAC-seq: Sample size when pooling sample reads to call peaks
atac-seq sample size Peak Normalize
6.3 years ago jaime.alvarez.benayas • 0
0
votes
0
replies
1.5k
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
4.8 years ago • updated 4.7 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
1.1k
views
Job: Bioinformatics Analyst II/III - Banchereau Lab @ The Jackson Laboratory
rnaseq atac-seq iso-seq chipseq Job
6.4 years ago tyler.chukwu • 0
0
votes
5
replies
1.4k
views
ATACSeqQC - error when splitting files using mm10
atacseqqc atac-seq R bioconductor rsamtools
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by • 0
0
votes
0
replies
1.1k
views
Centipede foot printing export
footprinting centipede atac-seq dnaseq
7.1 years ago rbronste ▴ 60
0
votes
4
replies
1.7k
views
ATAC-Seq peaks quality control with ChIPQC package, but getting error
ATAC-Seq ChIPQC
updated 5.2 years ago by 65k • written 5.2 years ago by ▴ 10
0
votes
0
replies
1.9k
views
Job: Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq atac-seq gro-seq bsseq rnaseq Job
8.5 years ago Jaritz,Markus ▴ 20
1
vote
1
reply
1.5k
views
DiffBind: How could I debug estimateDispersionsFit (required by DBA_DESEQ2)
atac-seq diffbind
7.0 years ago zhaolin20042008 • 0
0
votes
0
replies
933
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
4.3 years ago lhuang7 ▴ 50
42 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
United States, 2 minutes ago
Canada, 4 minutes ago
France, 7 minutes ago
France, 7 minutes ago
Germany, 9 minutes ago
Traffic: 1096 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