# Multi-Omics data integration

## Documentation for package ‘gINTomics’ version 1.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

create_multiassay | MultiAssayExperiment generation
dot_plotly | plotting enrichment
extract_model_res | Setting method for extracting results
extract_model_res-method | Setting method for extracting results
mirna_hsa | miRNA IDs. Dataset containing lastly definition of miRNAs (Names, Accessions, Sequences, Families and others) from different miRBase versions (From miRBase version 6 to version 22).
mmultiassay_ov | Example data for a standard workflow. This is an example dataset containing a MultiAssayExperiment of 20 ovarian cancer (OVC) patients extracted from the Cancer Genome Atlas (TCGA) database. The object contains all the available input data types: Gene expression data, miRNA expression data, gene methylation data, gene Copy Number Variations and miRNA Copy Number Variations.
MultiClass-class | MultiClass Class
MultiOmics-class | MultiOmics Class
plot_chr_distribution | plotting chr distribution
plot_heatmap | plotting heatmap
plot_network | Plotting network
plot_ridge | plotting ridge
plot_tf_distribution | plotting TF distribution
plot_venn | plotting venn
plot_volcano | plotting volcano
run_cnv_integration | Integration of expression and Copy Number Variations
run_genomic_enrich | Running genomic enrichment analysis
run_genomic_integration | Integration of expression, Copy Number Variations and methylation data
run_met_integration | Integration of expression and methylation
run_multiomics | Complete Multi-Omics integration
run_shiny | Start a Shiny application for integrated multi-omics data analysis.
run_tf_enrich | Running TF enrichment analysis
run_tf_integration | Integration of expression and Transcription Factors / Generic Regulators