README.md

rnaseq

A package to facilitate RNA-Seq analysis using pre-computed annotations.

Install

In R:

devtools::install_github("CharlesJB/rnaseq")

Main functions:

• import_kallisto
• get_raw_count_anno_df
• get_tpm_anno_df
• produce_pca
• deseq2_analysis

Please see documentation using the ? (i.e.: ?import_kallisto)

RUVg normalization

• ruvg_normalization

See also the use_ruv parameter of the deseq2_analysis function.