Banjo	Bayesian network inference with Java objects
BN	Bayesian network
CE	Community extraction
CLR	Context-likelihood-relatedness
CNA	Copy number aberration
CSPRV	Cancer subtype prediction using $R_2$
DAG	Directed acyclic graph
DEG	Differential expressed gene
DiME	Disease module extraction
DINGO	Differential network analysis in genomics
EMT	Epithelial-to-mesenchymal transition
EPoC	Endogenous perturbation analysis of cancer
GBM	Glioblastoma multiforme
GBM-BioDP	Glioblastoma Bio Discovery Portal
GEO	Gene Expression Omnibus
GMM	Gaussian mixture model
GO	Gene Ontology
GWAS	Genome-wide association study
HGG	High-grade glioma
IAMB	Incremental associated Markov blanket
IDA	Intervention calculus when the DAG is absent
iDINGO	Integrative differential network analysis in genomics
InTRINSiC	Integrative Modeling of Transcription Regulatory Interactions for
	Systematic Inference of Susceptibility in Cancer
KEGG	Kyoto Encyclopedia of Genes and Genomes
KINC	Knowledge Independent Network Construction
LGG	Low-grade glioma
TCGA	The Cancer Genome Atlas
CCLE	Cancer Cell Line Encyclopedia
CGGA	Chinese Glioma Genome Atlas
EN	Elastic net
lasso	Least absolute shrinkage selection operator
lncRNA	Long non-coding RNA
MI	Mutual information
MSLCRN	Module-specific lncRNA-mRNA causal regulatory networks
NGS	Next-generation sequencing
PDX	Patient-derived xenograft
RNA-seq	RNA sequencing
scRNA-seq	Single-cell RNA sequencing
SNF	Similarity Network Fusion
SNP	Single-nucleotide polymorphism
SYGNAL	Systems Genetics Network Analysis
TAM	Tumor-associated macrophage
TCI	Tumor-specific causal inference
TF	Transcriptional factor
TRN	Transcriptional regulatory network
twiner	Twin networks recovery
WGCNA	Weighted gene coexpression network analysis
WSNF	Weighted similarity network fusion