Showing : atac-seq • reset
0
votes
9
replies
480
views
No peak corresponding to the nucleosome-free regions is observed in Fragment size distribution of ATAC-seq
ATACseqQC Fragmentsizedistribution ATAC-seq
4 months ago Xiaojie Cheng • 0
3
votes
5
replies
481
views
csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 10 months ago by ▴ 10 • written 11 months ago by ▴ 30
0
votes
5
replies
391
views
ATACSeqQC - error when splitting files using mm10
atacseqqc atac-seq R bioconductor rsamtools
updated 16 months ago by 3.4k • written 16 months ago by • 0
2
votes
8
replies
410
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma edger atac atac-seq
updated 18 months ago by ★ 27k • written 19 months ago by ▴ 60
0
votes
0
replies
278
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
20 months ago lhuang7 ▴ 50
0
votes
0
replies
894
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
2.2 years ago • updated 2.1 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
537
views
Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 2.2 years ago by 6.5k • written 2.2 years ago by • 0
1
vote
11
replies
753
views
ATAC-QC shiftGAlignmentsList function
ATAC-seq ATACseqQC
updated 2.2 years ago by ★ 4.3k • written 2.2 years ago by • 0
0
votes
1
reply
272
views
ATAC-QC fragSizeDist function
ATAC-seq ATACseqQC
updated 2.2 years ago by ★ 4.3k • written 2.2 years ago by • 0
0
votes
6
replies
832
views
atacseqQC error while splittin the bamfile
ATACseqQC ATAC-seq error split bam file
updated 2.4 years ago by • 0 • written 2.4 years ago by • 0
0
votes
4
replies
603
views
How to produce the fraction of reads in peaks (FRiP) using DiffBind
DiffBind FRiP ATAC-Seq dba.show dba.count
updated 2.5 years ago by ★ 4.1k • written 2.5 years ago by ▴ 20
0
votes
0
replies
310
views
Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC ATAC-Seq Library complexity estimateLibComplexity
2.5 years ago Gary ▴ 20
2
votes
5
replies
553
views
The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC bamQC ATAC-Seq totalQNAMEs MAPQ
updated 2.6 years ago by ★ 4.3k • written 2.6 years ago by ▴ 20
11
votes
21
replies
2.4k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity
updated 2.6 years ago by ★ 4.3k • written 2.6 years ago by ▴ 20
0
votes
4
replies
843
views
ATAC-Seq peaks quality control with ChIPQC package, but getting error
ATAC-Seq ChIPQC
updated 2.6 years ago by 58k • written 2.6 years ago by ▴ 10
0
votes
1
reply
443
views
Use DiffBind to find differential peaks among multiple cell types
diffbind atac-seq differential analysis deseq2
updated 2.9 years ago by ★ 4.1k • written 2.9 years ago by • 0
3
votes
3
replies
568
views
Differential analysis of multiple samples with different time points
diffbind R atac-seq
updated 2.9 years ago by ★ 4.1k • written 2.9 years ago by • 0
2
votes
2
replies
540
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
3.4 years ago shankasal • 0
6
votes
9
replies
2.6k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 3.4 years ago by ★ 27k • written 3.4 years ago by • 0
0
votes
7
replies
1.0k
views
ATACseqQC memory overflow issue
atac-seq software error atacseqqc
updated 3.6 years ago by • 0 • written 3.6 years ago by ▴ 10
4
votes
6
replies
691
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 3.6 years ago by 34k • written 3.6 years ago by ▴ 60
0
votes
0
replies
812
views
ATAC-seq: Sample size when pooling sample reads to call peaks
atac-seq sample size Peak Normalize
3.7 years ago jaime.alvarez.benayas • 0
4
votes
3
replies
624
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 3.8 years ago by ★ 27k • written 3.8 years ago by ▴ 60
0
votes
0
replies
604
views
Job: Bioinformatics Analyst II/III - Banchereau Lab @ The Jackson Laboratory
rnaseq atac-seq iso-seq chipseq Job
3.8 years ago tyler.chukwu • 0
0
votes
6
replies
944
views
Warnings when update DiffBind and running errors
diffbind atac-seq dba.count
updated 3.8 years ago by ★ 4.1k • written 3.8 years ago by • 0
0
votes
1
reply
3.7k
views
Calling differential peaks from ATAC-seq data using DEseq2
deseq2 atac-seq
updated 3.8 years ago by ★ 4.1k • written 3.8 years ago by • 0
4
votes
3
replies
2.7k
views
Rsubread counting peaks ATACseq
Rsubread atac-seq narrowpeaks featurecounts
updated 3.8 years ago by ★ 3.3k • written 3.8 years ago by ▴ 80
1
vote
4
replies
885
views
DiffBind error with dba.count after update
diffbind read counting warning message chromatin atac-seq
updated 3.8 years ago by ▴ 640 • written 3.9 years ago by • 0
3
votes
9
replies
1.1k
views
Error When using dba.count() in DiffBind
dba.count atac-seq diffbind
updated 3.8 years ago by ▴ 640 • written 3.9 years ago by • 0
0
votes
1
reply
470
views
Error with dba.count function code
diffbind dba.count atac-seq
updated 3.9 years ago by ▴ 640 • written 3.9 years ago by • 0
0
votes
1
reply
913
views
Homer getDiffExpression.pl issue
homer atac-seq
updated 4.2 years ago by • 0 • written 4.2 years ago by • 0
0
votes
11
replies
1.0k
views
DiffBind: failed to run dba.count in SSH
SSH atac-seq
updated 4.4 years ago by ▴ 640 • written 4.4 years ago by • 0
1
vote
7
replies
2.1k
views
DiffBind R package issue
diffbind atac-seq
updated 4.4 years ago by ★ 4.1k • written 4.4 years ago by • 0
0
votes
6
replies
1.3k
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
4.4 years ago zhaolin20042008 • 0
1
vote
1
reply
783
views
DiffBind: How could I debug estimateDispersionsFit (required by DBA_DESEQ2)
atac-seq diffbind
4.4 years ago zhaolin20042008 • 0
1
vote
7
replies
1.8k
views
loading dba.plotVolcano in DiffBind
diffbind chipseq atac-seq rory stark
updated 4.4 years ago by ★ 4.1k • written 4.5 years ago by • 0
0
votes
0
replies
660
views
Centipede foot printing export
footprinting centipede atac-seq dnaseq
4.5 years ago rbronste ▴ 60
2
votes
3
replies
6.8k
views
DiffBind for ATAC-seq
atac-seq diffbind macs2 macs peak finding
updated 4.5 years ago by ▴ 20 • written 5.1 years ago by ▴ 40
3
votes
4
replies
1.5k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 4.6 years ago by 34k • written 4.6 years ago by ▴ 10
1
vote
4
replies
1.5k
views
DiffBind for open chromatin mapping
diffbind dnaseseq atac-seq
4.7 years ago rbronste ▴ 60
0
votes
3
replies
1.9k
views
DiffBind Normalization by bFullLibrarySize
atac-seq
updated 5.5 years ago by ★ 4.1k • written 5.5 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
5.9 years ago Jaritz,Markus ▴ 20
42 results • Page 1 of 1
Recent ...
Replies
Answer: Undefined columns error R cytometry analysis by Jiang, Mike ★ 1.3k
I see you are trying to fill the missing transform info to `gs_bcell_auto` , which is a hack, but since you seems to know what you are doin…
Comment: how to get MFI stats from data by Jiang, Mike ★ 1.3k
Can you grant the public caccess to you fcs to reproduce your issue?
Answer: Getting a dataset that only contains the flow data within the gated area by Jiang, Mike ★ 1.3k
You didn't post your example code, so here is my best guess of your workflow > library(flowCore) > library(flowWorkspace) …
Comment: Diffbind dba.plotProfile attempt to select less than one element in OneIndex by bhanratt • 0
``` > DBA 10 Samples, 31953 sites in matrix: ID Tissue Factor Condition Replicate Reads FRiP 1 58 1 H3K4me3 AD …
Answer: Warning messages on Apple M1 BigSur by Vincent J. Carey, Jr. 6.5k
We are not producing M1 binaries at this time. If you use the intel version of R under Rosetta 2 you can use the intel mac binaries.
Votes
Comment: Use of coef() as a measure of effect size in a multiple regression using DESeq2
Answer: Log fold change interpretation of time series with Wald test
A: gviz: name of tracks disappeas
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Awards • All
Scholar to Jiang, Mike ★ 1.3k
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Scholar to jbnrodriguez • 0
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