https://github.com/sigven/oncoenrichr
Explore the cancer relevance of your gene list
https://github.com/sigven/oncoenrichr
cancer cancer-hallmark-evidence cancer-survival co-expression crispr-target disease-gene-association functional-enrichment-analysis genesets high-throughput-screening pathway-enrichment-analysis prioritization protein-complexes protein-protein-interaction proteins report-generator tcga-data tissue-enrichment-analysis
Last synced: 8 days ago
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Explore the cancer relevance of your gene list
- Host: GitHub
- URL: https://github.com/sigven/oncoenrichr
- Owner: sigven
- License: other
- Created: 2019-11-21T07:53:42.000Z (over 6 years ago)
- Default Branch: main
- Last Pushed: 2025-12-17T10:06:54.000Z (6 months ago)
- Last Synced: 2026-02-27T05:02:50.642Z (3 months ago)
- Topics: cancer, cancer-hallmark-evidence, cancer-survival, co-expression, crispr-target, disease-gene-association, functional-enrichment-analysis, genesets, high-throughput-screening, pathway-enrichment-analysis, prioritization, protein-complexes, protein-protein-interaction, proteins, report-generator, tcga-data, tissue-enrichment-analysis
- Language: R
- Homepage: https://sigven.github.io/oncoEnrichR/
- Size: 1.9 GB
- Stars: 52
- Watchers: 5
- Forks: 10
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
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README
# oncoEnrichR 
**oncoEnrichR** is an R package for functional interrogation of human gene lists
in the context of cancer. The package leverages an extensive amount of prior
molecular knowledge that allows for biological interpretation along
multiple dimensions, both at the systems level and at the level of individual genes.
Web-based access to **oncoEnrichR** (through the [Galaxy platform](https://usegalaxy.org/)) is available at
[**https://oncotools.elixir.no**](https://oncotools.elixir.no/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fsigven%2Foncoenrichr%2Foncoenrichr_wrapper%2F1.6.1).
_The web version of oncoEnrichR is not currently operating with the latest version,
we are working to get the latest version in place also in Galaxy._
**oncoEnrichR** is primarily intended for exploratory analysis and prioritization
of a gene list (referred to here as **query set**) from high-throughput cancer
biology experiments, e.g. CRISPR screens, protein proximity labeling, or gene
expression profiling. In principle, oncoEnrichR can be relevant for any screen
or analysis that produces a list of human gene _hits_ that needs functional
annotation and/or prioritization with respect to cancer relevance. The tool
queries a number of high-quality data resources in order to assemble
cancer-relevant annotations and analyses in an interactive report.
## Getting started
- [What types of questions can be answered by oncoEnrichR?](https://sigven.github.io/oncoEnrichR/index.html#questions-addressed-by-oncoenrichr)
- [Output views from oncoEnrichR](https://sigven.github.io/oncoEnrichR/articles/output.html)
- [Installation instructions](https://sigven.github.io/oncoEnrichR/articles/installation.html)
- [Running instructions](https://sigven.github.io/oncoEnrichR/articles/running.html)
- [Annotation resources available in oncoEnrichR](https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html)
## News
- December 16th 2025: [**1.6.1 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-6-1)
- September 19th 2025: [**1.6.0 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-6-0)
- February 27th 2025: [**1.5.3 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-5-3)
- September 9th 2024: [**1.5.2 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-5-2)
## Example report
## Citation
If you use oncoEnrichR, please cite the following publication:
Sigve Nakken, Sveinung Gundersen, Fabian L. M. Bernal, Dimitris Polychronopoulos, Eivind Hovig, and Jørgen Wesche. **Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR** (2023). Int J Cancer. [doi:10.1002/ijc.34666](https://doi.org/10.1002/ijc.34666)
### Contact
sigven AT ifi.uio.no
### Funding and Collaboration
oncoEnrichR is supported by the [Centre for Cancer Cell Reprogramming](https://www.med.uio.no/cancell/english/) at the [University of Oslo](https://www.uio.no)/[Oslo University Hospital](https://radium.no), and [Elixir Norway (Oslo node)](https://elixir.no/organization/organisation/elixir-uio).
