Reference

run Function for running the full workflow in one step
runAll()	run all step in default setting
Pre Check Function for checking your data
pre_check()	Pre-check you data by PCA and Heat maps
DEG Analysis Functions for DEG analysis by limma edgeR and DESeq2
DEG_container-class	a S4 class
deg_DESeq2()	Run DEseq2
deg_edgeR()	Run degeR
deg_limma()	Run limma
deg_run()	run DEG
run_DESeq2()	Basic produce of DESeq2
run_edgeR()	Basic produce of edgeR
run_limma()	Basic produce of limma
GO Functions for enrichment analysis of GO
enrichGO_run()	Enrichment analysis of go
enrich_go()	enrich_go
enhance_enrichGO()	GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.
enhance_enricher_internal()	enrich.internal
KEGG Functions for enrichment analysis of KEGG
enrichKEGG_run()	Enrichment analysis of kegg
enrich_kegg()	enrich_go
gseKEGG Functions for enrichment analysis of gseKEGG
enrichgesKEGG_run()	run enrichgesKEGG
enrich_gsekegg()	gseKEGG from DEG data
Visualizations Functions for Visualizations
barplot_base()	barplot_base
barplot_base2()	barplot_base2
enhance_barplot()	Enhanced barplot
enhance_gseplot()	plot gseKEGG plot
geskegg_barplot()	gseKEGG bar plot
kegg_barplot()	KEGG bar plot
enhance_heatmap()	Heatmap for DEG data frame
enhance_volcano()	enhance_volcano
Tools Functions for data processing
cut_much()	cut data
top_deg()	Choose top genes from DEG data frame
Example Data Some sample data
counts_input	An example dataset
go_res	An example dataset
group_list	An example dataset
DEG_df	An example dataset