Bioconductor Atac

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637

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ATACSeq peaks ATAC ChIPpeakAnno

10 months ago Raghad • 0

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1.2k

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rna-seq Read10X_h5 atac modalities

updated 24 months ago by James W. MacDonald 68k • written 24 months ago by Cynthia • 0

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948

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ATAC DiffBind ATACSeq

updated 2.1 years ago by Rory Stark ★ 5.2k • written 2.1 years ago by Hadar • 0

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diffbind atac

updated 4.8 years ago by Rory Stark ★ 5.2k • written 4.8 years ago by lindsaynhayes • 0

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723

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r DiffBind ATAC

updated 5.1 years ago by Rory Stark ★ 5.2k • written 5.1 years ago by lindsaynhayes • 0

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2.0k

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limma edger atac atac-seq

updated 5.1 years ago by Aaron Lun ★ 28k • written 5.1 years ago by pgugger ▴ 70

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987

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deseq2 design formula design matrix edgeR ATAC

updated 5.3 years ago by Gordon Smyth 52k • written 5.3 years ago by corinne_hutfilz • 0

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Diffbind ATAC batch correction blocking factor

updated 5.6 years ago by Rory Stark ★ 5.2k • written 5.6 years ago by rm1238 • 0

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ATACseqQC ATAC ATACseq software error Tutorial

updated 5.8 years ago by Steve Lianoglou ★ 13k • written 5.8 years ago by mbasam • 0

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3.8k

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subread featurecounts atac

updated 6.0 years ago by Wei Shi ★ 3.6k • written 6.0 years ago by aurel.nagy ▴ 10

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diffbind ATACseq ATAC counts differential analysis

updated 6.0 years ago by Rory Stark ★ 5.2k • written 6.0 years ago by pgontarz ▴ 10

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2.6k

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diffbind atac

updated 6.1 years ago by Rory Stark ★ 5.2k • written 6.1 years ago by paz2005 • 0

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diffbind atac

7.8 years ago niu.shengyong ▴ 10

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5.2k

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ATAC differential binding analysis no replicates DEseq2 chromatin

8.0 years ago BioinfGuru ▴ 70

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1.6k

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Diffbind Atac adapters

updated 8.0 years ago by Rory Stark ★ 5.2k • written 8.0 years ago by BioinfGuru ▴ 70

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atac-seq atac deseq2 sva combat

updated 8.1 years ago by Michael Love 43k • written 8.1 years ago by g.atla ▴ 10

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6.9k

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 9.8 years ago by Gordon Smyth 52k • written 9.9 years ago by samuel collombet ▴ 140

17 results • Page 1 of 1

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Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k

If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…

Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k

Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …

Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k

We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…

Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k

It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…

Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20

I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…

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Looking for equivalent EPIC chip v1 vs. v2 annotation variables

Properly constructing a hypergeometric test

A: Is logFC a log2 fold change or some other base in scran::findMarkers

Comment: Error in retrieving clinical data

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