Bioconductor Knitr

Showing : knitr • reset

votes

502

views

RStudio MOFA2 bug knitr

updated 11 months ago by James W. MacDonald 63k • written 11 months ago by Kevin Coombes ▴ 430

votes

replies

617

views

knitr boxplot

updated 3.7 years ago by James W. MacDonald 63k • written 3.7 years ago by poojitha.stemcell ▴ 10

vote

966

views

rmarkdown knitr

updated 4.6 years ago by Aaron Lun ★ 28k • written 4.6 years ago by Keith Hughitt ▴ 180

votes

replies

15k

views

rmarkdown rstudio knitr

7.0 years ago Jon Bråte ▴ 250

votes

replies

1.7k

views

software error knitr

updated 7.3 years ago by Martin Morgan 25k • written 7.3 years ago by idomtamir ▴ 10

votes

1.2k

views

knitr vignettes built bioccheck no-ASCII

7.5 years ago kmezhoud ▴ 10

6 results • Page 1 of 1

Recent ...

Replies

Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k

Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.

Comment: collapseReplicates error after tximeta by Michael Love 40k

A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…

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 …

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