Biostar ATAC

Showing : ATAC • reset

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4.6k

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 7.0 years ago by Gordon Smyth 45k • written 7.0 years ago by samuel collombet ▴ 140

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3.5k

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ATAC differential binding analysis no replicates DEseq2 chromatin

5.2 years ago YaGalbi ▴ 20

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1.9k

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atac-seq atac deseq2 sva combat

updated 5.2 years ago by Michael Love 37k • written 5.2 years ago by g.atla ▴ 10

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579

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diffbind ATACseq ATAC counts differential analysis

updated 3.2 years ago by Rory Stark ★ 4.4k • written 3.2 years ago by pgontarz ▴ 10

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563

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limma edger atac atac-seq

updated 2.2 years ago by Aaron Lun ★ 27k • written 2.2 years ago by pgugger ▴ 60

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1.6k

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diffbind atac

updated 3.3 years ago by Rory Stark ★ 4.4k • written 3.3 years ago by paz2005 • 0

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496

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diffbind atac

updated 2.0 years ago by Rory Stark ★ 4.4k • written 2.0 years ago by lindsaynhayes • 0

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2.6k

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diffbind atac

5.0 years ago niu.shengyong • 0

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1.4k

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subread featurecounts atac

updated 3.1 years ago by Wei Shi ★ 3.4k • written 3.1 years ago by aurel.nagy ▴ 10

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174

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r DiffBind ATAC

updated 2.2 years ago by Rory Stark ★ 4.4k • written 2.2 years ago by lindsaynhayes • 0

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286

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deseq2 design formula design matrix edgeR ATAC

updated 2.4 years ago by Gordon Smyth 45k • written 2.4 years ago by corinne_hutfilz • 0

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854

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ATACseqQC ATAC ATACseq software error Tutorial

updated 2.9 years ago by Steve Lianoglou 13k • written 2.9 years ago by mbasam • 0

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1.0k

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Diffbind Atac adapters

updated 5.2 years ago by Rory Stark ★ 4.4k • written 5.2 years ago by YaGalbi ▴ 20

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402

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Diffbind ATAC batch correction blocking factor

updated 2.8 years ago by Rory Stark ★ 4.4k • written 2.8 years ago by rm1238 • 0

14 results • Page 1 of 1

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Comment: ashr vs apeglm for interaction data by Ali Barry ▴ 30

Thanks, I'll trying playing a bit there. I have done some minor filtering already (requiring at least 5 counts in 10% of my samples, across…

Comment: ashr vs apeglm for interaction data by Michael Love 37k

I see why apeglm is conservative— the dispersion is very high within group. An idea would be to use ashr but do some additional filtering …

Comment: How to figure out the FC value from Limma by ATpoint ★ 1.2k

That’s an Excel problem, not a GEO/R problem or related to limma and Bioconductor.

Comment: ashr vs apeglm for interaction data by Ali Barry ▴ 30

Hi Michael, Plots attached. Many of the large fold changes with `ashr` are driven by one sample per group, but a few are maybe a bit more …

Comment: regression analysis for epic array methylation data using limma by nabiyogesh ▴ 10

Thanks! I have tried this; I am not sure after that how to find logeGFR associated probe? and also, how to filter significant probe? …

Votes

Answer: How to properly use DESeq2 for an experiment

Comment: ashr vs apeglm for interaction data

Comment: How to figure out the FC value from Limma

Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2

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