Bioconductor ATAC

Showing : ATAC • reset

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143

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rna-seq Read10X_h5 atac modalities

updated 10 weeks ago by James W. MacDonald 63k • written 10 weeks ago by Cynthia • 0

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185

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ATAC DiffBind ATACSeq

updated 3 months ago by Rory Stark ★ 4.9k • written 4 months ago by Hadar • 0

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787

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diffbind atac

updated 3.0 years ago by Rory Stark ★ 4.9k • written 3.1 years ago by lindsaynhayes • 0

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361

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r DiffBind ATAC

updated 3.3 years ago by Rory Stark ★ 4.9k • written 3.3 years ago by lindsaynhayes • 0

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917

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limma edger atac atac-seq

updated 3.3 years ago by Aaron Lun ★ 28k • written 3.3 years ago by pgugger ▴ 70

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464

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deseq2 design formula design matrix edgeR ATAC

updated 3.5 years ago by Gordon Smyth 47k • written 3.5 years ago by corinne_hutfilz • 0

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608

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Diffbind ATAC batch correction blocking factor

updated 3.8 years ago by Rory Stark ★ 4.9k • written 3.8 years ago by rm1238 • 0

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1.3k

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ATACseqQC ATAC ATACseq software error Tutorial

updated 4.0 years ago by Steve Lianoglou 13k • written 4.0 years ago by mbasam • 0

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2.1k

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subread featurecounts atac

updated 4.2 years ago by Wei Shi ★ 3.5k • written 4.2 years ago by aurel.nagy ▴ 10

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888

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diffbind ATACseq ATAC counts differential analysis

updated 4.2 years ago by Rory Stark ★ 4.9k • written 4.2 years ago by pgontarz ▴ 10

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1.9k

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diffbind atac

updated 4.3 years ago by Rory Stark ★ 4.9k • written 4.3 years ago by paz2005 • 0

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3.6k

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diffbind atac

6.0 years ago niu.shengyong • 0

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4.0k

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ATAC differential binding analysis no replicates DEseq2 chromatin

6.2 years ago BioinfGuru ▴ 20

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1.2k

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Diffbind Atac adapters

updated 6.2 years ago by Rory Stark ★ 4.9k • written 6.2 years ago by BioinfGuru ▴ 20

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2.3k

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atac-seq atac deseq2 sva combat

updated 6.3 years ago by Michael Love 40k • written 6.3 years ago by g.atla ▴ 10

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5.3k

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 8.0 years ago by Gordon Smyth 47k • written 8.1 years ago by samuel collombet ▴ 140

16 results • Page 1 of 1

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Answer: multiple filters in biomaRt by RuBBiT0 ▴ 10

First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use. Second, could you pro…

Comment: Diffbind "No genome detected" by kyliecode • 0

Hi Dr. Stark, Thanks very much for your reply! The bam files were output from nf-core/chipseq pipeline and for some reason, they do not ha…

Answer: Discrepancy between DESeq2 files produced in Galaxy and R(RStudio) by Michael Love 40k

I guess that Galaxy may be using some kind of LFC shrinkage, but without seeing their code I wouldn't know for sure. Shrinkage generally…

Comment: TCGAbiolinks cannot find bcr_patient_barcode by Habil Zare ▴ 170

I checked your example with the devel version 2.29.6 on Bioc and it worked fine. Thanks for the fix!

Answer: error in ChAMP loading file by jenniferbrowngates • 0

I got a lot of information from this website about different topics which is beneficial for me too so I thank this site and also suggest a …

Votes

Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)

Comment: Error: biomaRt has encountered an unexpected server error.

Comment: Interpret plot from DiffBind

Awards • All

Scholar to Tiago C. Silva ▴ 270