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driverpower

DriverPower

https://github.com/smshuai/driverpower

Science Score: 20.0%

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
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary

Keywords

bioinformatics genomics
Last synced: 11 months ago · JSON representation

Repository

DriverPower

Basic Info
  • Host: GitHub
  • Owner: smshuai
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 106 MB
Statistics
  • Stars: 26
  • Watchers: 2
  • Forks: 4
  • Open Issues: 7
  • Releases: 0
Topics
bioinformatics genomics
Created almost 10 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

A tool for computational cancer driver discovery

Github version GitHub license Platform conda Documentation Status

Installation | Tutorial | Documentation

DriverPower is a tool used to discover potential coding and non-coding cancer driver elements from tumour whole-genome or whole-exome somatic mutations.

How to use DriverPower

If you only have somatic mutations (in hg19) at hand and would like to find drivers in well-annotated regions, please use our example data and follow the tutorial.

Citation

Please cite our paper when you use DriverPower in your study:

  • Shuai S, PCAWG Drivers and Functional Interpretation Working Group, Gallinger S, Stein L & PCAWG Consortium (2020) Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nat. Commun. 11: 734–734 Available at: https://www.ncbi.nlm.nih.gov/pubmed/32024818

Please cite the PCAWG driver paper as well when you use our example data in your study:

  • Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, et al (2020) Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 578: 102–111 Available at: https://www.ncbi.nlm.nih.gov/pubmed/32025015

License

DriverPower is distributed under the terms of the GNU General Public License 3.0.

Change log

  • 2018/09/12: Release version 1.0.2, which has some minor modifications.
  • 2017/11/22: Release version 1.0.1, which has bugs fixes and improved performance.
  • 2017/08/03: Release version 1.0.0, which is used in our manuscript.
  • 2017/03/02: Release version 0.4.0, which is used in the PCAWG driver analysis.

GitHub Events

Total
  • Watch event: 1
  • Push event: 1
Last Year
  • Watch event: 1
  • Push event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 261
  • Total Committers: 7
  • Avg Commits per committer: 37.286
  • Development Distribution Score (DDS): 0.605
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
sshuai s****i@m****a 103
Shimin Shuai s****n@g****m 103
Shimin Shuai s****i@o****a 51
Shimin Shuai s****i@h****a 1
Shimin Shuai s****i@h****a 1
smshuai s****i@g****m 1
Shimin Shuai s****i@h****a 1
Committer Domains (Top 20 + Academic)
hn6.hpc.oicr.on.ca: 1 hn7.hpc.oicr.on.ca: 1 hn1.hpc.oicr.on.ca: 1 oicr.on.ca: 1 mail.utoronto.ca: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 10
  • Total pull requests: 11
  • Average time to close issues: about 2 months
  • Average time to close pull requests: less than a minute
  • Total issue authors: 9
  • Total pull request authors: 2
  • Average comments per issue: 3.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 1
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: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • yasunorikogure (2)
  • ningwei-wei (1)
  • corner0426 (1)
  • Slavatron (1)
  • THT-sleepy (1)
  • xuebingjie1990 (1)
  • alhafidzhamdan (1)
  • ysbioinfo (1)
  • t-silvers (1)
Pull Request Authors
  • smshuai (10)
  • dependabot[bot] (2)
Top Labels
Issue Labels
Pull Request Labels
dependencies (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 30 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 5
  • Total maintainers: 1
pypi.org: driverpower

Combined burden and functional test for coding and noncoding cancer drivers

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 30 Last month
Rankings
Dependent packages count: 10.1%
Stargazers count: 12.3%
Forks count: 15.4%
Average: 17.4%
Dependent repos count: 21.6%
Downloads: 27.9%
Maintainers (1)
smshuai
Last synced: 11 months ago

Dependencies

setup.py pypi
  • numpy *
  • pandas *
  • pybedtools *
  • scikit-learn *
  • scipy *
  • statsmodels *
  • tables *
  • xgboost *