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driveR

Prioritizing Cancer Driver Genes Using Genomics Data

https://github.com/egeulgen/driver

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
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    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (18.2%) to scientific vocabulary

Keywords

cancer-driverness driver driver-gene-prioritization identify-driver-genes ranking-genes scoring
Last synced: 6 months ago · JSON representation

Repository

Prioritizing Cancer Driver Genes Using Genomics Data

Basic Info
Statistics
  • Stars: 17
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Topics
cancer-driverness driver driver-gene-prioritization identify-driver-genes ranking-genes scoring
Created over 5 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

#  driveR: An R Package for Prioritizing Cancer Driver Genes Using Genomics Data


[![CRAN version](http://www.r-pkg.org/badges/version-ago/driveR)](https://cran.r-project.org/package=driveR)
[![R-CMD-check](https://github.com/egeulgen/driveR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/egeulgen/driveR/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/egeulgen/driveR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/egeulgen/driveR?branch=master)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)


Cancer genomes contain large numbers of somatic alterations but few genes drive tumor development. Identifying cancer driver genes is critical for precision oncology. Most of current approaches either identify driver genes based on mutational recurrence or using estimated scores predicting the functional consequences of mutations. 

`driveR` is a tool for personalized or batch analysis of genomics data for driver gene prioritization by combining genomics information and prior biological knowledge. As features, driveR uses coding impact metaprediction scores, non-coding impact scores, somatic copy number alteration scores, hotspot gene/double-hit gene condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG pathways. It uses these features to estimate cancer-type-specific probabilities for each gene of being a cancer driver using the related task of a multi-task learning classification model.

The method is described in detail in _Ülgen E, Sezerman OU. driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. BMC Bioinformatics. 2021 May 24;22(1):263.[https://doi.org/10.1186/s12859-021-04203-7](https://doi.org/10.1186/s12859-021-04203-7)_ 

## Installation

You can install the latest released version of `driveR` from CRAN via:

```r
install.packages("driveR")
```


You can install the development version of `driveR` from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("egeulgen/driveR", build_vignettes = TRUE)
```

## Usage

![driveR workflow](https://github.com/egeulgen/driveR/blob/master/inst/extdata/driver_workflow.png?raw=true "driveR workflow")

`driveR` has two main objectives:

1. Prediction of **impact of coding variants** (achieved via `predict_coding_impact()`)
2. **Prioritization of cancer driver genes** (achieved via `create_features_df()` and `prioritize_driver_genes()`)

Note that `driveR` require operations outside of R and depends on the outputs from the external tools `ANNOVAR` and `phenolyzer`.

For detailed information on how to use `driveR`, please see the vignette "How to use driveR" via `vignette("how_to_use")`

Owner

  • Name: Ege Ulgen
  • Login: egeulgen
  • Kind: user
  • Location: London
  • Company: @genomicsengland

MD, PhD - Bioinformatics Engineer

GitHub Events

Total
  • Watch event: 2
Last Year
  • Watch event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 207
  • Total Committers: 1
  • Avg Commits per committer: 207.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 8
  • Committers: 1
  • Avg Commits per committer: 8.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Ege Ulgen e****n@g****m 207

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 7
  • Total pull requests: 1
  • Average time to close issues: 8 months
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • egeulgen (7)
Pull Request Authors
  • egeulgen (1)
Top Labels
Issue Labels
enhancement (2) bug (1)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 180 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
cran.r-project.org: driveR

Prioritizing Cancer Driver Genes Using Genomics Data

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 180 Last month
Rankings
Stargazers count: 15.6%
Forks count: 21.9%
Dependent packages count: 29.8%
Average: 31.4%
Dependent repos count: 35.5%
Downloads: 54.1%
Maintainers (1)
egeulgen@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • GenomeInfoDb * imports
  • GenomicFeatures * imports
  • GenomicRanges * imports
  • S4Vectors * imports
  • TxDb.Hsapiens.UCSC.hg19.knownGene * imports
  • TxDb.Hsapiens.UCSC.hg38.knownGene * imports
  • caret * imports
  • org.Hs.eg.db * imports
  • randomForest * imports
  • rlang * imports
  • covr * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests