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cleaver

Cleavage of polypeptide sequences

https://github.com/sgibb/cleaver

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
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 13 committers (7.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.6%) to scientific vocabulary

Keywords

bioc cleavage digest peptides r

Keywords from Contributors

bioconductor-packages genomics gene mass-spectrometry metabolomics bioconductor proteomics bioinformatics feature-detection looking-for-maintainer
Last synced: 9 months ago · JSON representation

Repository

Cleavage of polypeptide sequences

Basic Info
Statistics
  • Stars: 13
  • Watchers: 2
  • Forks: 3
  • Open Issues: 0
  • Releases: 0
Topics
bioc cleavage digest peptides r
Created about 13 years ago · Last pushed about 2 years ago
Metadata Files
Readme

README.md

cleaver

Project Status: Active - The project has reached a stable, usable state and is being actively developed. build status codecov.io license

years in bioc Ranking by downloads Release: build release Devel: build devel <!-- badges: end -->

Description

This package cleaves polypeptide sequences. The cleavage rules are taken from: https://web.expasy.org/peptidecutter/peptidecutterenzymes.html

cleaver is part of Bioconductor.

Install development version (not recommended)

r install.packages("devtools") library("devtools") install_github("sgibb/cleaver")

Usage

```r

load library

library("cleaver")

Gastric juice peptide 1 (UniProtKB/Swiss-Prot: GAJU_HUMAN/P01358)

gaju <- "LAAGKVEDSD"

cleave(gaju, "trypsin")

$LAAGKVEDSD

[1] "LAAGK" "VEDSD"

cleave(gaju, "trypsin", missedCleavages=1)

$LAAGKVEDSD

[1] "LAAGKVEDSD"

cleave(gaju, "trypsin", missedCleavages=0:1)

$LAAGKVEDSD

[1] "LAAGK" "VEDSD" "LAAGKVEDSD"

cleave(gaju, "pepsin")

$LAAGKVEDSD

[1] "LAAGKVEDSD"

(no cleavage)

```

Owner

  • Name: Sebastian Gibb
  • Login: sgibb
  • Kind: user
  • Location: Greifswald, Germany
  • Company: University Medicine Greifswald

GitHub Events

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

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 125
  • Total Committers: 13
  • Avg Commits per committer: 9.615
  • Development Distribution Score (DDS): 0.672
Past Year
  • Commits: 9
  • Committers: 2
  • Avg Commits per committer: 4.5
  • Development Distribution Score (DDS): 0.222
Top Committers
Name Email Commits
s.gibb u****n 41
Sebastian Gibb m****l@s****e 33
Dan Tenenbaum d****a@f****g 16
Nitesh Turaga n****a@g****m 14
Herve Pages h****s@f****g 5
J Wokaty j****y@s****u 4
Hervé Pagès h****s@f****g 2
Marc Carlson m****n@f****g 2
vobencha v****n@r****g 2
vobencha v****a@g****m 2
J Wokaty j****y 2
Martin Morgan m****n@f****g 1
Sonali Arora s****a@f****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 5 roswellpark.org: 1 fredhutch.org: 1 sph.cuny.edu: 1 sebastiangibb.de: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 7
  • Total pull requests: 0
  • Average time to close issues: 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 4
  • Total pull request authors: 0
  • Average comments per issue: 1.71
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
  • sgibb (3)
  • pavel-shliaha (2)
  • manogenome (1)
  • jeanmanguy (1)
Pull Request Authors
Top Labels
Issue Labels
TODO (3) wontfix (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 42,289 total
  • Total dependent packages: 2
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: cleaver

Cleavage of Polypeptide Sequences

  • Versions: 5
  • Dependent Packages: 2
  • Dependent Repositories: 0
  • Downloads: 42,289 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 9.5%
Downloads: 28.6%
Maintainers (1)
mail@sebastiangibb.de
Last synced: 9 months ago

Dependencies

DESCRIPTION cran
  • Biostrings >= 1.29.8 depends
  • R >= 3.0.0 depends
  • methods * depends
  • IRanges * imports
  • S4Vectors * imports
  • BRAIN * suggests
  • BiocStyle >= 0.0.14 suggests
  • UniProt.ws >= 2.1.4 suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 0.8 suggests
.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite