In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Basic Default Worflow

library(RNAseqStat)
results_dir = "test"

run all in one time

runAll will run full workflow in default parameters

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

This step contains following 5 steps, more detail parameters can be set in following functions.

Check your data

This step is useful to quickly check you data. dir Can be any wherr you want to save results file.

pre_check(counts_data = counts_input, group_list = group_list, dir = results_dir)

DEG analysis

DEG analysis will be run by limma edgeR and DESeq2 in this step.

deg_run(counts_input,group_list,test_group = "T", control_group = "C",dir = results_dir)

GO

Enrichment analysis of GO will be done in this Step.

enrichGO_run(DEG_df, x = "log2FoldChange", y = "pvalue", dir = results_dir)

KEGG

Enrichment analysis of KEGG will be done in this Step.

enrichKEGG_run(DEG_df, x = "log2FoldChange", y = "pvalue", dir = results_dir)

GSEA

enrichgesKEGG_run(DEG_df, x = "log2FoldChange", dir = results_dir)

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