Showing : ATAC-Seq • reset
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 10 months ago by ★ 4.9k • written 11 months ago by • 0
0
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9
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5.3k
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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
4.4 years ago • updated 4.3 years ago Xiaojie Cheng • 0
3
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5
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3.7k
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csaw for ATAC, quantitation of Tn5 insertion sites only
csaw ATAC-seq Tn5 insertions
updated 4.8 years ago by ▴ 10 • written 4.9 years ago by ▴ 50
0
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5
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2.0k
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ATACSeqQC - error when splitting files using mm10
atacseqqc atac-seq R bioconductor rsamtools
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
2
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8
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2.2k
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Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma edger atac atac-seq
updated 5.5 years ago by ★ 29k • written 5.5 years ago by ▴ 70
0
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Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
5.7 years ago lhuang7 ▴ 50
0
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0
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1.8k
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
6.2 years ago • updated 6.0 years ago Julie Zhu ★ 4.3k
0
votes
1
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1.4k
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Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 6.1 years ago by ★ 6.5k • written 6.1 years ago by • 0
1
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11
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3.3k
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ATAC-QC shiftGAlignmentsList function
ATAC-seq ATACseqQC
updated 6.1 years ago by ★ 4.3k • written 6.1 years ago by • 0
0
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1
reply
1.4k
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ATAC-QC fragSizeDist function
ATAC-seq ATACseqQC
updated 6.1 years ago by ★ 4.3k • written 6.1 years ago by • 0
0
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6
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2.6k
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atacseqQC error while splittin the bamfile
ATACseqQC ATAC-seq error split bam file
updated 6.3 years ago by • 0 • written 6.3 years ago by ▴ 10
0
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4
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2.7k
views
How to produce the fraction of reads in peaks (FRiP) using DiffBind
DiffBind FRiP ATAC-Seq dba.show dba.count
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by ▴ 20
0
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0
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Enough cell number or not based on library complexity evaluation by ATACseqQC?
ATACseqQC ATAC-Seq Library complexity estimateLibComplexity
6.4 years ago Gary ▴ 20
2
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5
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2.0k
views
The meaning of results produced by the bamQC function implemented in the ATACseqQC
ATACseqQC bamQC ATAC-Seq totalQNAMEs MAPQ
updated 6.5 years ago by ★ 4.3k • written 6.5 years ago by ▴ 20
11
votes
21
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6.9k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity
updated 6.6 years ago by ★ 4.3k • written 6.6 years ago by ▴ 20
0
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4
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2.3k
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ATAC-Seq peaks quality control with ChIPQC package, but getting error
ATAC-Seq ChIPQC
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 10
0
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1
reply
1.6k
views
Use DiffBind to find differential peaks among multiple cell types
diffbind atac-seq differential analysis deseq2
updated 6.8 years ago by ★ 5.2k • written 6.8 years ago by • 0
3
votes
3
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1.8k
views
Differential analysis of multiple samples with different time points
diffbind R atac-seq
updated 6.9 years ago by ★ 5.2k • written 6.9 years ago by • 0
2
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2
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1.7k
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CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
7.3 years ago shankasal • 0
6
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9
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7.0k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
0
votes
7
replies
2.9k
views
ATACseqQC memory overflow issue
atac-seq software error atacseqqc
updated 7.5 years ago by • 0 • written 7.6 years ago by ▴ 10
4
votes
6
replies
2.0k
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 60
0
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0
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2.1k
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ATAC-seq: Sample size when pooling sample reads to call peaks
atac-seq sample size Peak Normalize
7.6 years ago jaime.alvarez.benayas • 0
4
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3
replies
1.6k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 7.7 years ago by ★ 29k • written 7.7 years ago by ▴ 60
0
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0
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1.5k
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Job: Bioinformatics Analyst II/III - Banchereau Lab @ The Jackson Laboratory
rnaseq atac-seq iso-seq chipseq Job
7.7 years ago tyler.chukwu • 0
0
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6
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2.6k
views
Warnings when update DiffBind and running errors
diffbind atac-seq dba.count
updated 7.8 years ago by ★ 5.2k • written 7.8 years ago by • 0
0
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1
reply
6.8k
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Calling differential peaks from ATAC-seq data using DEseq2
deseq2 atac-seq
updated 7.8 years ago by ★ 5.2k • written 7.8 years ago by • 0
5
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3
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6.7k
views
Rsubread counting peaks ATACseq
Rsubread atac-seq narrowpeaks featurecounts
updated 7.8 years ago by ★ 3.6k • written 7.8 years ago by ▴ 90
1
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4
replies
2.7k
views
DiffBind error with dba.count after update
diffbind read counting warning message chromatin atac-seq
updated 7.8 years ago by ▴ 670 • written 7.8 years ago by • 0
3
votes
9
replies
3.5k
views
Error When using dba.count() in DiffBind
dba.count atac-seq diffbind
updated 7.8 years ago by ▴ 670 • written 7.8 years ago by • 0
0
votes
1
reply
1.4k
views
Error with dba.count function code
diffbind dba.count atac-seq
updated 7.9 years ago by ▴ 670 • written 7.9 years ago by • 0
0
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1
reply
2.7k
views
Homer getDiffExpression.pl issue
homer atac-seq
updated 8.1 years ago by • 0 • written 8.2 years ago by ▴ 10
0
votes
11
replies
2.7k
views
DiffBind: failed to run dba.count in SSH
SSH atac-seq
updated 8.3 years ago by ▴ 670 • written 8.3 years ago by • 0
1
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7
replies
4.4k
views
DiffBind R package issue
diffbind atac-seq
updated 8.4 years ago by ★ 5.2k • written 8.4 years ago by ▴ 10
0
votes
6
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3.5k
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
8.4 years ago zhaolin20042008 • 0
1
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1
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1.9k
views
DiffBind: How could I debug estimateDispersionsFit (required by DBA_DESEQ2)
atac-seq diffbind
8.4 years ago zhaolin20042008 • 0
1
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7
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3.3k
views
loading dba.plotVolcano in DiffBind
diffbind chipseq atac-seq rory stark
updated 8.4 years ago by ★ 5.2k • written 8.4 years ago by • 0
0
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0
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1.4k
views
Centipede foot printing export
footprinting centipede atac-seq dnaseq
8.4 years ago rbronste ▴ 60
2
votes
3
replies
10k
views
DiffBind for ATAC-seq
atac-seq diffbind macs2 macs peak finding
updated 8.5 years ago by ▴ 70 • written 9.0 years ago by ▴ 50
3
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4
replies
3.6k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 8.5 years ago by 43k • written 8.5 years ago by ▴ 10
1
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4
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2.7k
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DiffBind for open chromatin mapping
diffbind dnaseseq atac-seq
8.6 years ago rbronste ▴ 60
0
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3
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3.2k
views
DiffBind Normalization by bFullLibrarySize
atac-seq
updated 9.5 years ago by ★ 5.2k • written 9.5 years ago by ▴ 10
0
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0
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2.2k
views
Job: Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq atac-seq gro-seq bsseq rnaseq Job
9.8 years ago Jaritz,Markus ▴ 20
43 results • Page 1 of 1
Recent ...
Replies
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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