Showing : ATAC-Seq • reset
0
votes
9
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3.4k
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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
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
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
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 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 70
0
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0
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930
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
0
votes
0
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1.4k
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
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
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
1
reply
942
views
ATAC-QC fragSizeDist function
ATAC-seq ATACseqQC
updated 4.8 years ago by ★ 4.3k • written 4.8 years ago by • 0
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
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 ★ 5.1k • written 5.1 years ago by ▴ 20
0
votes
0
replies
764
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
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
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
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
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 ★ 5.1k • written 5.5 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 ★ 5.1k • written 5.5 years ago by • 0
2
votes
2
replies
1.2k
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
5.9 years ago shankasal • 0
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
0
votes
7
replies
2.1k
views
ATACseqQC memory overflow issue
atac-seq software error atacseqqc
updated 6.2 years ago by • 0 • written 6.2 years ago by ▴ 10
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
0
votes
0
replies
1.6k
views
ATAC-seq: Sample size when pooling sample reads to call peaks
atac-seq sample size Peak Normalize
6.2 years ago jaime.alvarez.benayas • 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
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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
6
replies
2.0k
views
Warnings when update DiffBind and running errors
diffbind atac-seq dba.count
updated 6.4 years ago by ★ 5.1k • written 6.4 years ago by • 0
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 ★ 5.1k • written 6.4 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
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
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 6.4 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
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
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
1
vote
7
replies
3.6k
views
DiffBind R package issue
diffbind atac-seq
updated 7.0 years ago by ★ 5.1k • written 7.0 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
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
1
vote
7
replies
2.7k
views
loading dba.plotVolcano in DiffBind
diffbind chipseq atac-seq rory stark
updated 7.0 years ago by ★ 5.1k • written 7.0 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
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 7.6 years ago by ▴ 40
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
1
vote
4
replies
2.2k
views
DiffBind for open chromatin mapping
diffbind dnaseseq atac-seq
7.2 years ago rbronste ▴ 60
0
votes
3
replies
2.6k
views
DiffBind Normalization by bFullLibrarySize
atac-seq
updated 8.1 years ago by ★ 5.1k • written 8.1 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
42 results • Page 1 of 1
Recent ...
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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