README.md

oncoEnrichR - cancer-dedicated gene set interpretation

Contents

Overview

oncoEnrichR is an R package for functional interrogation of human genesets in the context of cancer.

The package is intended for exploratory analysis and prioritization of a gene list (referred to as query set below) from high-throughput cancer biology experiments, e.g. genetic screens (siRNA/CRISPR), protein proximity labeling, or transcriptomics (differential expression). The tool queries a number of high-quality data resources in order to assemble useful gene annotations and analyses in an interactive report. The contents of the final report attempts to shed light on the following questions:

News

Annotation resources

Data harvested from the following resources form the backbone of oncoEnrichR:

Example report

DOI

Getting started

Installation

  1. install.packages('devtools')
  2. devtools::install_github('sigven/oncoEnrichR')
  3. library(oncoEnrichR)

stable

Usage

oncoEnrichR performs its operations through the following procedures/methods:

1. oncoEnrichR::onco_enrich()

2. oncoEnrichR::write()

Example run

A target list of n = 134 high-confidence interacting proteins with the c-MYC oncoprotein were previously identified through BioID protein proximity assay in standard cell culture and in tumor xenografts (Dingar et al., J Proteomics, 2015). We ran this target list through the oncoEnrichR analysis workflow using the following configurations for the onco_enrich method:

and produced the following HTML report with results.

Below are R commands provided to reproduce the example output. NOTE: Replace "LOCAL_FOLDER" with a directory on your local computer:

Contact

sigven AT ifi.uio.no

Funding & collaboration

OncoEnrichR is supported by the Centre for Cancer Cell Reprogramming at the University of Oslo/Oslo University Hospital, and Elixir Norway (Oslo node).

       



sigven/oncoEnrichR documentation built on April 9, 2021, 9:06 p.m.