In amcdavid/GeneseeBulk: Pipeline, analysis functions and markdown templates for bulk RNAseq

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

GeneseeBulk

The goal of GeneseeBulk is to facilitate analysis (differential expression) of Bulk RNASeq.

Installation

You can install the development version of GeneseeBulk from GitHub with:

# install.packages("devtools")
devtools::install_github("amcdavid/GeneseeBulk")

Example

The Genesee* family of packages is organized around project templates that copy over various parametrized markdown scripts.
As such, there's some code required to set overall parameters for the project.

library(GeneseeBulk)
dir.create(tmp <- tempfile())
proj_directory = Genesee::genesee_skeleton(genesee_root = tmp,
                          investigator = 'Plato', 
                          project_title = 'Crito',
                          project_type = 'RNA',
                          init_git = FALSE)

After that, you would edit 00driver.R to customize how the markdown are run.

Templates

At the moment, there are r length(list.files(proj_directory, pattern = '*.Rmd')) template available:

list.files(proj_directory, pattern = '*.Rmd')

You can browse the files here.

amcdavid/GeneseeBulk documentation built on March 26, 2022, 4:58 a.m.