In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

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

RNAseqStat

The goal of RNAseqStat is a workflow for DEG analysis.

Installation

You can install the released version of RNAseqStat from CRAN with:

install.packages("RNAseqStat")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("xiayh17/RNAseqStat")

Example

This is a basic example which shows you how to solve a common problem:

library(RNAseqStat)
## basic example code

run all in one time

runAll will run full workflow in default parameters.

This include 5 steps:

1. Check your data
2. DEG analysis
3. GO
4. KEGG
5. GSEA

runAll(count_data = counts_input, group_list = group_list, 
       test_group = "T", control_group = "C",
       OrgDb = 'org.Hs.eg.db', dir = results_dir)

Every step can be run separately.

Your can check more in xiayh17.top/rnaseqstat

xiayh17/RNAseqStat documentation built on June 16, 2022, 11:51 a.m.