Pre-requested R packages

R version >= 3.6.0

The following is a description of the dependent R packages, mainly to help developers better understand the code in NetBID2.

The users does not need to digest the information below.

R package	Functions1	Category	Purpose
Biobase	-	Data processing	ExpressionSet class
GEOquery	getGEO	Data processing	Get expression dataset from GEO database
limma	-	Data processing	Expression data normalization
impute	impute.knn	Data processing	Data imputation
tximport	Data processing	Data import
DESeq2	DESeqDataSetFromTximport,DESeq	Data processing	Data import from txi and normalization for RNASeq data
ConsensusClusterPlus	-	Clustering	Get consensus clustering results
aricode	clustComp	Clustering	For cluster comparison statistic calculation
igraph	-	Visualization	Igraph class and basic network-based calculation
RColorBrewer	brewer.pal	Visualization	Get color bar
plot3D	scatter3D	Visualization	3D plot
plotrix	draw.ellipse	Visualization	Drawing ellipse
umap	umap	Visualization	Data dimension reduction and visualization
ComplexHeatmap	Heatmap	Visualization	Heatmap drawing
plotly	-	Visualization	For interactive plot
ordinal	clm,clmm	bid	Cumulative link mixed models
MCMCglmm	MCMCglmm	bid	Multivariate generalized linear mixed models
arm	bayesglm	bid	Bayesian generalized linear models
reshape	melt	bid	Melt an object into a form suitable for easy casting
biomaRt	-	ID conversion	ID conversion
GSVA	gsva	Gene Set	Gene set activity calculation
msigdbr	-	Gene Set	MSigDB database
openxlsx	-	IO	Output into EXCEL file (master table)
rhdf5	H5Fopen,H5Fclose	IO	For hd5 formation data processing (MICA)
rmarkdown	render	Report	For generating HTML report file
kableExtra	-	Report	For table layout in the report file

1. ’-‘ in the Function column represents multiple functions in the package were used in NetBID2. ↩