Biostar ATAC

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2.6k

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diffbind atac

5.0 years ago • updated 4.9 years ago niu.shengyong • 0

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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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282

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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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3.5k

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ATAC differential binding analysis no replicates DEseq2 chromatin

5.2 years ago YaGalbi ▴ 20

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572

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diffbind ATACseq ATAC counts differential analysis

updated 3.1 years ago by Rory Stark ★ 4.4k • written 3.2 years ago by pgontarz ▴ 10

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1.4k

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subread featurecounts atac

updated 3.1 years ago by Wei Shi ★ 3.3k • written 3.1 years ago by aurel.nagy ▴ 10

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399

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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

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559

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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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171

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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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484

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diffbind atac

updated 24 months ago by Rory Stark ★ 4.4k • written 24 months ago by lindsaynhayes • 0

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1.9k

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atac-seq atac deseq2 sva combat

updated 5.2 years ago by Michael Love 36k • written 5.2 years ago by g.atla ▴ 10

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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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1.6k

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diffbind atac

updated 3.2 years ago by Rory Stark ★ 4.4k • written 3.2 years ago by paz2005 • 0

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848

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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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Comment: Variance explained (coefficient of determination) in edgeR by Gordon Smyth 45k

The R2 values look completely normal. The median R2 is 10%, which seems somewhat low rather than high. With so many genes, you will natural…

Comment: Variance explained (coefficient of determination) in edgeR by Gemma • 0

Many thanks, that seems to work! However, the estimates tend to be surprisingly high, for many genes R2 being close to 1 (quartiles being…

Answer: EnrichGO not working with db created from annotationhub by Lucía • 0

I've gone through my code and I'm pretty sure the issue is not the code, but that some gene IDs (all the ones that start with LOC) are just…

Comment: DiffBind GreyListChIP error: Error: BiocParallel errors by ksong • 0

Hi Rory, Thank you for your reply! Here is the my `sessionInfo()`: Please let me know what you think. I really appreciate your help! …

Comment: EnrichGO not working with db created from annotationhub by Lucía • 0

I used the gtf file from ncbi Here: https://www.ncbi.nlm.nih.gov/assembly/GCF_900626175.2/ Everything was taken from there

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Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0

Answer: Use MulticoreParam under BatchtoolsParam

Answer: Variance explained (coefficient of determination) in edgeR

HTSeq Counts no longer available

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Popular Question to Johannes Rainer ★ 1.9k