README.md

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

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)
#> Creating /var/folders/33/vpk59z855zzbrczltjnc52qh0000gn/T//RtmpStz8dl/file807925494e3f/Plato
#> Creating /var/folders/33/vpk59z855zzbrczltjnc52qh0000gn/T//RtmpStz8dl/file807925494e3f/Plato/Crito
#> Creating /var/folders/33/vpk59z855zzbrczltjnc52qh0000gn/T//RtmpStz8dl/file807925494e3f/Plato/Crito/rawdata
#> Creating /var/folders/33/vpk59z855zzbrczltjnc52qh0000gn/T//RtmpStz8dl/file807925494e3f/Plato/Crito/refined
#> Now symlink or copy raw data to /var/folders/33/vpk59z855zzbrczltjnc52qh0000gn/T//RtmpStz8dl/file807925494e3f/Plato/Crito/rawdata and run make_sample_sheet.

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

project_title='Crito'
authors = 'default'
type = 'RNA'

# devtools::load_all("path/to/GeneseeBulk")
# devtools::load_all("path/to/Genesee")

## or
library(GeneseeBulk)
library(Genesee)

#### set up directories and create sample file
geneseesc_skeleton(main_directory, investigator, project_title, authors = authors, project_type = type)

rmarkdown::render('01_load.Rmd', params = list( input_tsv = "deSeq_counts.txt",
                                                input_project = NULL,
                                                sample_sheet_csv= "all_samples_file.csv",
                                                output_root= "refined/01load"),  output_dir = 'reports')

Templates

At the moment, there are 2 template available:

list.files(proj_directory, pattern = '*.Rmd')
#> [1] "01_load.Rmd"   "02_qc_dea.Rmd"

You can browse the files here.

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