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CNVMetrics

R Package to compare copy number variant (CNV) results from multiple samples/methods

https://github.com/krasnitzlab/cnvmetrics

Science Score: 23.0%

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 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 8 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.5%) to scientific vocabulary

Keywords

cnv copy-number-variation metrics package r r-language r-package

Keywords from Contributors

bioconductor-packages grna-sequence gene bioconductor genomics ontologies sequencing immune-repertoire synthetic-nucleosomes simulator
Last synced: 6 months ago · JSON representation

Repository

R Package to compare copy number variant (CNV) results from multiple samples/methods

Basic Info
Statistics
  • Stars: 4
  • Watchers: 1
  • Forks: 2
  • Open Issues: 4
  • Releases: 6
Topics
cnv copy-number-variation metrics package r r-language r-package
Created over 7 years ago · Last pushed over 2 years ago
Metadata Files
Readme

README.md

R-CMD-check-bio codecov License: Artistic-2.0

CNVMetrics

The CNVMetrics package offers multiple quantitative metrics of similarity between copy number profiles. Among these are metrics based on CNV status calls only (amplification/deletion status) or on the level of amplification/deletion. In addition, a visualization tool is provided to explore resulting metrics.

Citing ##

If you use this package for a publication, we would ask you to cite the following:

Belleau P, Deschênes A, Beyaz S et al. CNVMetrics package: Quantifying similarity between copy number profiles [version 1; not peer reviewed]. F1000Research 2021, 10:737 (slides) (doi: 10.7490/f1000research.1118704.1)

F1000Research poster

Authors

Astrid Deschênes, Pascal Belleau, David A. Tuveson and Alexander Krasnitz

Bioconductor Package

Bioconductor Time

The CNVMetrics package is now an official package of Bioconductor.

The current release can be directly downloaded from their website: Current release

However, all official releases can be downloaded from this site: All releases

Documentation

CNVMetrics Website

CNVMetrics Get Started

Installation

To install this package from Bioconductor, start R (version "4.2") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CNVMetrics")

To install the latest version accessible using the devtools package:

 ## Load required package
 library(devtools)

 ## Install the latest version of CNVMetrics
 devtools::install_github('KrasnitzLab/CNVMetrics')

License

This package and the underlying CNVMetrics code are distributed under the Artistic license 2.0. You are free to use and redistribute this software.

For more information on Artistic 2.0 License see http://opensource.org/licenses/Artistic-2.0

Bugs/Feature requests

Please contact us for bug fixes or with feature requests.

Thanks!

Owner

  • Name: KrasnitzLab
  • Login: KrasnitzLab
  • Kind: organization

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 366
  • Total Committers: 8
  • Avg Commits per committer: 45.75
  • Development Distribution Score (DDS): 0.101
Past Year
  • Commits: 8
  • Committers: 5
  • Avg Commits per committer: 1.6
  • Development Distribution Score (DDS): 0.75
Top Committers
Name Email Commits
Astrid Deschenes a****n@h****m 329
Astrid Deschenes a****n@@h****m 17
Astrid Deschenes a****n 11
Nitesh Turaga n****a@g****m 2
J Wokaty j****y@s****u 2
belleau p****u@h****m 2
J Wokaty j****y 2
belleau b****u@b****u 1
Committer Domains (Top 20 + Academic)
belleaumbp.cshl.edu: 1 sph.cuny.edu: 1 : 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 11
  • Total pull requests: 51
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 4 hours
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.55
  • Merged pull requests: 51
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 6.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • adeschen (10)
  • gevro (1)
Pull Request Authors
  • adeschen (49)
  • belleau (2)
Top Labels
Issue Labels
enhancement (6) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 5,835 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: CNVMetrics

Copy Number Variant Metrics

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 5,835 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 30.1%
Downloads: 90.4%
Maintainers (1)
adeschen@hotmail.com
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.1 depends
  • BiocParallel * imports
  • GenomicRanges * imports
  • IRanges * imports
  • S4Vectors * imports
  • grDevices * imports
  • gridExtra * imports
  • magrittr * imports
  • methods * imports
  • pheatmap * imports
  • stats * imports
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests