Bioconductor Rnaseq analysis

Showing : rnaseq analysis • reset

votes

replies

3.6k

views

rnaseq analysis variancestabilizingtransformation normalization cpm edger

updated 6.9 years ago by Wolfgang Huber ★ 13k • written 6.9 years ago by svlachavas ▴ 840

votes

replies

4.5k

views

deseq2 timecourse multiple factor design RNAseq analysis differential gene expression

updated 7.5 years ago by Gavin Kelly ▴ 690 • written 7.5 years ago by c.nicole ▴ 50

vote

replies

2.3k

views

limma differential gene expression rnaseq analysis alignment RSEM

updated 7.3 years ago by Aaron Lun ★ 28k • written 7.3 years ago by goldberg.jm ▴ 10

votes

replies

861

views

rnaseq analysis

updated 6.2 years ago by James W. MacDonald 68k • written 6.2 years ago by marak • 0

votes

replies

2.3k

views

filterByExpression edgeR RNAseq analysis edger

updated 5.0 years ago by Gordon Smyth 52k • written 5.0 years ago by hcnbox • 0

5 results • Page 1 of 1

Recent ...

Replies

Comment: CpGs with genomic positions greater than the chromosome size in EPICv2? by Joshua Llano • 0

Thank you for your reply James. I was worried that it was my mistake.

Comment: Annotation package for Manduca sexta by GA ▴ 10

Thank you!

Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k

If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…

Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k

Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …

Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k

We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…

Votes

Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?

Answer: Explannation for ROAST results

A: How DiffBind run PCA based on peak data?

Looking for equivalent EPIC chip v1 vs. v2 annotation variables

Properly constructing a hypergeometric test

Awards • All

Supporter to bhanu.chandra1 • 0