Bioconductor Repitools

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repitools promoter tss annotation

7.7 years ago Ryan C. Thompson ★ 7.9k

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repitools bioconductor cpgDensityCalc

8.6 years ago divyswar01 • 0

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Baymeth methylation MBD-seq Repitools

9.5 years ago pm2015 • 0

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repitools

10.4 years ago Matthias Lienhard ▴ 280

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BSgenome BSgenome Repitools BSgenome BSgenome Repitools

11.7 years ago Dario Strbenac ★ 1.6k

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BSgenome BSgenome Repitools BSgenome BSgenome Repitools

11.8 years ago Jaritz,Markus ▴ 20

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GO Repitools GO Repitools

updated 12.0 years ago by Dario Strbenac ★ 1.6k • written 12.0 years ago by Tim Smith ★ 1.1k

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limma Repitools limma Repitools

12.8 years ago Guest User ★ 13k

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Alignment convert Repitools Alignment convert Repitools

updated 2.0 years ago by Marge • 0 • written 12.9 years ago by José Luis Lavín ▴ 280

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BSgenome BSgenome Repitools BSgenome BSgenome Repitools

updated 14.1 years ago by Chao-Jen Wong ▴ 580 • written 14.1 years ago by Guest User ★ 13k

10 results • Page 1 of 1

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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k

BTW, I tested with no issue on MacOS ARM on our previous github issue.

Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k

The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…

Answer: PTM analysis in LIMPA by Gordon Smyth 53k

For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…

Answer: problem reading bam files into nucleR by James W. MacDonald 68k

The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…

Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k

It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …

Votes

C: DESeq2 Following RSEM

Upcoming Ensembl API and data access changes - new blog post available

Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

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Commentator to sina.nassiri ▴ 130