README.md

In jamieobrett/multiomics: Analysis of Multiple Molecular Datasets of Different Types

This is an R package developed to integrate analysis of multiple types of molecular profiling data (transcriptomics, proteomics, metabolomics, and epigenomics). It loads and deduplicates data, converts identifiers, performs enrichment/overrepresentation analysis on individual datasets, and combines these analyses with rank aggregation. There are multiple options for each step.

This software depends on the following R packages:

From CRAN:

igraph
httr
RankAggreg
RobustRankAggreg

From BioConductor:

org.Mm.eg.db
AnnotationDbi
EnrichmentBrowser
rWikiPathways
PGSEA

It comes bundled with GSEA_4.0.3 and JDK11 for running GSEA.

To install:

git clone https://github.com/jamieobrett/multiomics.git

Then open R

devtools::document(pkg="path/to/multiomics")
devtools::install(pkg="path/to/multiomics")
library(multiomics)

jamieobrett/multiomics documentation built on Oct. 19, 2023, 8:21 p.m.