Bioconductor StageR

Showing : StageR • reset

votes

422

views

stageR

updated 23 months ago by Koen Van den Berge ▴ 180 • written 23 months ago by giwa.ao • 0

votes

669

views

DRIMSeq stageR

updated 4.6 years ago by Koen Van den Berge ▴ 180 • written 4.6 years ago by sdvie • 0

votes

replies

1.4k

views

stageR rnaseqDTU DRIMSeq DEXSeq

4.7 years ago d-joester ▴ 20

votes

replies

993

views

limma stageR decideTests

updated 4.7 years ago by Koen Van den Berge ▴ 180 • written 4.7 years ago by maltethodberg ▴ 170

votes

replies

854

views

drimseq rnaseqdtu stager

updated 4.8 years ago by Michael Love 40k • written 4.8 years ago by Jack.Hearn • 0

vote

replies

1.2k

views

DEXSeq StageR rnaseqDTU

updated 4.9 years ago by Michael Love 40k • written 5.0 years ago by rbenel ▴ 30

votes

replies

1.4k

views

drimseq stageR dtu salmon rna seq

updated 5.2 years ago by Koen Van den Berge ▴ 180 • written 5.2 years ago by fiona.dick91 ▴ 60

7 results • Page 1 of 1

Recent ...

Replies

Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k

Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…

Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k

Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…

Votes

Comment: Batch correction and repeated measures

batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

Awards • All