Bioconductor Chipseq

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2.9k

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DiffBind chipseq

updated 9 months ago by Rory Stark ★ 5.2k • written 9 months ago by ANAMIKA • 0

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1.8k

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DiffBind R chipseq

updated 4 months ago by Rory Stark ★ 5.2k • written 6.6 years ago by kyliecode • 0

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1.1k

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diffbind chipseq

updated 11 months ago by lin.pei26 • 0 • written 4.7 years ago by danielaperry2015 • 0

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1.1k

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ChIPpeakAnno ChIPSeq

updated 8 months ago by James W. MacDonald 65k • written 8 months ago by Jerina ▴ 10

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996

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ChIPSeq DiffBind

updated 10 months ago by Rory Stark ★ 5.2k • written 11 months ago by lin.pei26 • 0

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592

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ChIPSeq annotate ChIPpeakAnno

updated 12 months ago by Kai Hu ▴ 70 • written 12 months ago by C T ▴ 140

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434

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DiffBind chipseq

updated 6 months ago by James W. MacDonald 65k • written 6 months ago by lin.pei26 • 0

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375

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chipseq DifferentialMethylation DESeq2

updated 12 weeks ago by Michael Love 41k • written 3 months ago by rebw25 • 0

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320

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csaw ChIPseq DiffBind

5 months ago jared.andrews07 ▴ 30

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274

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ChIPpeakAnno ChIPSeq MotifDiscovery

7 months ago franciscrick41 • 0

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165

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bSubControl ChIPSeq DiffBind

3 months ago frueher • 0

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150

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ChIPSeq annotation ChIPpeakAnno

11 weeks ago nilanjanamani88 • 0

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chipseq

updated 9 days ago by James W. MacDonald 65k • written 9 days ago by zhulin • 0

13 results • Page 1 of 1

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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…

Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

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

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

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?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0