https://github.com/bhklab/consensusov

Implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer.

Science Score: 23.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
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Academic publication links
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Committers with academic emails
1 of 11 committers (9.1%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (8.1%) to scientific vocabulary

Keywords

cancer-data cancer-genomics cancer-research expression-database ovarian-cancer

Keywords from Contributors

bioconductor-package genomics gene transcriptomics pharmacogenomic pharmacogx peak-detection ontology u24ca289073 copynumber

Last synced: 11 months ago · JSON representation

Repository

Implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer.

Basic Info

Host: GitHub
Owner: bhklab
Language: R
Default Branch: master
Homepage:
Size: 47.3 MB

Statistics

Stars: 3
Watchers: 3
Forks: 1
Open Issues: 4
Releases: 2

Topics

cancer-data cancer-genomics cancer-research expression-database ovarian-cancer

Created about 9 years ago · Last pushed over 2 years ago

Metadata Files

Readme Changelog

README.md

Bioc-Release: Bioconductor RELEASE

Bioc-Devel: Bioconductor DEVEL

Overview

This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.

Author: Gregory M Chen, Lavanya Kannan, Ludwig Geistlinger, Victor Kofia, Levi Waldron, Benjamin Haibe-Kains

Installation

``` r

Installing the development version from GitHub:

install.packages("devtools")

devtools::install_github("bhklab/consensusOV")

Installing the release version from Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("consensusOV") ```

Usage

Extensive usage examples are provided in the consensusOV vignette on Bioconductor: consensusOV.pdf

Getting help

Owner

Name: BHKLAB
Login: bhklab
Kind: organization
Location: Toronto, Ontario, Canada

Website: http://www.pmgenomics.ca/bhklab/
Repositories: 168
Profile: https://github.com/bhklab

The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre

GitHub Events

Total

Watch event: 1
Pull request event: 1
Fork event: 1

Last Year

Watch event: 1
Pull request event: 1
Fork event: 1

Committers

Last synced: about 1 year ago

All Time

Total Commits: 112
Total Committers: 11
Avg Commits per committer: 10.182
Development Distribution Score (DDS): 0.768

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
ChristopherEeles	c**s@o**m	26
kofiav	v**a@g**m	22
gmchen	g**n@g**m	18
Nitesh Turaga	n**a@g**m	14
lgeistlinger	l**r@b**e	11
Jermiah	j**8@g**m	8
J Wokaty	j**y@s**u	6
vobencha	v**a@g**m	2
Hervé Pagès	h**s@f**g	2
vobencha	v**n@r**g	2
Martin Morgan	m**n@f**g	1

Committer Domains (Top 20 + Academic)

fhcrc.org: 1 roswellpark.org: 1 fredhutch.org: 1 sph.cuny.edu: 1 bio.ifi.lmu.de: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time

Total issues: 17
Total pull requests: 41
Average time to close issues: about 1 year
Average time to close pull requests: about 5 hours
Total issue authors: 4
Total pull request authors: 4
Average comments per issue: 1.24
Average comments per pull request: 0.05
Merged pull requests: 36
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

kofiav (6)
lgeistlinger (2)
laetitiacollet (2)
lwaldron (1)

Pull Request Authors

kofiav (19)
lgeistlinger (3)
jjjermiah (2)
bd4everyone (2)

Top Labels

Issue Labels

warning (5) error (1)

Pull Request Labels

enhancement (1) warning (1)

Dependencies

DESCRIPTION cran

R >= 3.6 depends
Biobase * imports
GSVA * imports
gdata * imports
genefu * imports
limma * imports
matrixStats * imports
methods * imports
randomForest * imports
stats * imports
utils * imports
BiocStyle * suggests
ggplot2 * suggests
knitr * suggests
magick * suggests
rmarkdown * suggests

.github/workflows/R-CMD-check-bioc.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact v2 composite
docker/build-push-action v1 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite