Bioconductor Atac

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6.1k

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 8.9 years ago by Gordon Smyth 50k • written 8.9 years ago by samuel collombet ▴ 140

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ATAC differential binding analysis no replicates DEseq2 chromatin

7.1 years ago BioinfGuru ▴ 30

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2.8k

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atac-seq atac deseq2 sva combat

updated 7.2 years ago by Michael Love 41k • written 7.2 years ago by g.atla ▴ 10

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1.3k

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diffbind ATACseq ATAC counts differential analysis

updated 5.1 years ago by Rory Stark ★ 5.2k • written 5.1 years ago by pgontarz ▴ 10

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2.2k

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diffbind atac

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

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1.4k

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limma edger atac atac-seq

updated 4.2 years ago by Aaron Lun ★ 28k • written 4.2 years ago by pgugger ▴ 70

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diffbind atac

updated 3.9 years ago by Rory Stark ★ 5.2k • written 3.9 years ago by lindsaynhayes • 0

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2.9k

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subread featurecounts atac

updated 5.0 years ago by Wei Shi ★ 3.6k • written 5.0 years ago by aurel.nagy ▴ 10

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4.8k

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diffbind atac

6.9 years ago niu.shengyong • 0

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548

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r DiffBind ATAC

updated 4.1 years ago by Rory Stark ★ 5.2k • written 4.1 years ago by lindsaynhayes • 0

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670

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rna-seq Read10X_h5 atac modalities

updated 13 months ago by James W. MacDonald 65k • written 13 months ago by Cynthia • 0

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1.4k

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Diffbind Atac adapters

updated 7.1 years ago by Rory Stark ★ 5.2k • written 7.1 years ago by BioinfGuru ▴ 30

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ATACseqQC ATAC ATACseq software error Tutorial

updated 4.8 years ago by Steve Lianoglou ★ 13k • written 4.8 years ago by mbasam • 0

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939

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Diffbind ATAC batch correction blocking factor

updated 4.7 years ago by Rory Stark ★ 5.2k • written 4.7 years ago by rm1238 • 0

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764

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deseq2 design formula design matrix edgeR ATAC

updated 4.4 years ago by Gordon Smyth 50k • written 4.4 years ago by corinne_hutfilz • 0

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647

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ATAC DiffBind ATACSeq

updated 14 months ago by Rory Stark ★ 5.2k • written 14 months ago by Hadar • 0

16 results • Page 1 of 1

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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre

Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k

Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…

Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0

Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0