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clipper

A tool to identify CLIP-seq peaks

https://github.com/yeolab/clipper

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
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    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
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    Committers with academic emails
    6 of 13 committers (46.2%) from academic institutions
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (9.5%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

A tool to identify CLIP-seq peaks

Basic Info
  • Host: GitHub
  • Owner: YeoLab
  • License: other
  • Language: Python
  • Default Branch: master
  • Size: 417 MB
Statistics
  • Stars: 69
  • Watchers: 37
  • Forks: 43
  • Open Issues: 53
  • Releases: 0
Created almost 14 years ago · Last pushed about 3 years ago
Metadata Files
Readme License

README.md

CLIPper - CLIP peak enrichment recognition

A tool to detect CLIP-seq peaks.

Please visit our wiki page to learn more about usage of clipper: https://github.com/YeoLab/clipper/wiki/CLIPper-Home

Installation

```shell script

recreate PYTHON3 conda environment

cd clipper conda env create -f environment3.yml conda activate clipper3 pip install . ```

Alternative installation

  1. Thanks @rekado for making clipper available at GNU Guix guix install clipper
  2. We notice installation might be failing in some platform. Dockerized clipper is in the eclip repository here.

Command Line Usage

```shell script

shows all the options

clipper -h

minimal command

clipper -b YOURBAMFILE.bam -o YOUROUTFILE.bed -s hg19 ````

Run test

shell script cd clipper/clipper/test python -m unittest discover Right now the test coverage is still not 100%. And some subprocess warnings are not handled.

Frequently Asked Questions:

  1. How do use additional reference genome? See here for instructions: Supporting additional species

  2. Where can I use specify the Input bam file? Currently CLIPper does include input normalization. The input normalization pipeline is in another repository: Merge Peaks

Questions and suggestions

please open an issue in the repo. or email Charlene hsher@ucsd.edu

Reference

Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol. 2009;16(2):130-137. doi:10.1038/nsmb.1545

Lovci MT, Ghanem D, Marr H, et al. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol. 2013;20(12):1434-1442. doi:10.1038/nsmb.2699

Owner

  • Name: Yeo lab at UCSD
  • Login: YeoLab
  • Kind: organization
  • Location: United States of America

GitHub Events

Total
  • Issues event: 2
  • Watch event: 6
  • Issue comment event: 3
  • Fork event: 1
Last Year
  • Issues event: 2
  • Watch event: 6
  • Issue comment event: 3
  • Fork event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 628
  • Total Committers: 13
  • Avg Commits per committer: 48.308
  • Development Distribution Score (DDS): 0.492
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Gabriel Pratt g****t@u****u 319
spikesd17 m****i@g****m 120
gpratt g****t@g****m 101
Brian Yee b****1@u****u 21
algaebrown X****a 20
Hsuan-lin Her h****r@u****u 11
Hsuan-lin Her b****9@t****w 10
Jill-Moore J****e@u****u 9
Gabriel Pratt gpratt@ucsd.edu g****t@o****t 8
Alain Domissy a****y@g****m 5
Gabriel Pratt g****t@g****m 2
kstangline k****e@e****m 1
ppliu p****u@u****u 1
Committer Domains (Top 20 + Academic)
ucsd.edu: 4 eclipsebio.com: 1 oolite.calit2.optiputer.net: 1 umassmed.edu: 1 tmu.edu.tw: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 94
  • Total pull requests: 11
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 16 days
  • Total issue authors: 69
  • Total pull request authors: 6
  • Average comments per issue: 2.93
  • Average comments per pull request: 0.36
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 2.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gpratt (6)
  • ShanSabri (4)
  • mlovci (4)
  • algaebrown (3)
  • jalalsiddiqui (3)
  • mattgeorge28 (3)
  • gnilihzeux (2)
  • rekado (2)
  • gk7279 (2)
  • sangoc (2)
  • MattBrauer (2)
  • junjunlab (2)
  • omarwagih (2)
  • EricDeveaud (2)
  • byee4 (1)
Pull Request Authors
  • alaindomissy (5)
  • algaebrown (2)
  • kstangline (1)
  • gpratt (1)
  • Jill-Moore (1)
  • y9c (1)
Top Labels
Issue Labels
upgrade (6) options (5) bug (5) enhancement (4) question (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 97 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 5
  • Total versions: 2
  • Total maintainers: 2
pypi.org: clipper

A set of scripts for calling peaks on CLIP-seq data

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 5
  • Downloads: 97 Last month
Rankings
Forks count: 6.4%
Dependent repos count: 6.7%
Stargazers count: 8.9%
Dependent packages count: 10.0%
Average: 11.6%
Downloads: 25.8%
Maintainers (2)
algaebrown gpratt
Last synced: 11 months ago