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drawProteins

Creating package to draw proteins from Uniprot API

https://github.com/brennanpincardiff/drawproteins

Science Score: 10.0%

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
  • ✓
    Committers with academic emails
    1 of 6 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.3%) to scientific vocabulary

Keywords from Contributors

bioconductor-package illumina bioinformatics gene ontology rpackage genome-browser ncbi-geo high-dimensional genomics
Last synced: 11 months ago · JSON representation

Repository

Creating package to draw proteins from Uniprot API

Basic Info
  • Host: GitHub
  • Owner: brennanpincardiff
  • License: other
  • Language: R
  • Default Branch: master
  • Size: 895 KB
Statistics
  • Stars: 35
  • Watchers: 2
  • Forks: 19
  • Open Issues: 21
  • Releases: 0
Created about 9 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

Build Status

Coverage Status

Overview of drawProteins

This package has been created to allow the visualisation of protein schematics based on the data obtained from the Uniprot Protein Database.

The basic workflow is:

  • to provide one or more Uniprot IDs
  • get a list of features from the Uniprot API
  • draw the basic chains of these proteins
  • add features as desired

    drawProteins uses the package httr to interact with the Uniprot API and extract a JSON object into R. The JSON object is used to create a data.table.

    The graphing package ggplot2 is then used to create the protein schematic.

    The Vignette gives a good overview of the package.

    Sample script on R for Biochemists blog

    The master version of this package is available through Bioconductor. The development version is currently available here through GitHub.

    To install and use development branch:

    This package is available through Bioconductor. Installation instructions and documentation are available.

    To install from Github:

    {r, eval = FALSE} if (!require(devtools)) { install.packages('devtools') } dev_mode(on=TRUE) devtools::install_github('brennanpincardiff/drawProteins')

    Please cite the following article when using drawProteins:

    Brennan P. drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics [version 1; referees: 2 approved]. F1000Research 2018, 7:1105

    Feedback is very welcome. Please raise Github issues to provide bug reports, give feedback or request features.

    • Owner

    • Name: Paul Brennan
    • Login: brennanpincardiff
    • Kind: user
    • Location: Cardiff, UK
    • Company: Cardiff University

    GitHub Events

    Total
    • Watch event: 1
    • Fork event: 2
    Last Year
    • Watch event: 1
    • Fork event: 2

    Committers

    Last synced: almost 3 years ago

    All Time
    • Total Commits: 150
    • Total Committers: 6
    • Avg Commits per committer: 25.0
    • Development Distribution Score (DDS): 0.093
    Past Year
    • Commits: 0
    • Committers: 0
    • Avg Commits per committer: 0.0
    • Development Distribution Score (DDS): 0.0
    Top Committers
    Name Email Commits
    Paul Brennan b****f@g****m 136
    Nitesh Turaga n****a@g****m 6
    Stevin Wilson s****w@c****u 3
    vobencha v****a@g****m 2
    vobencha v****n@r****g 2
    daniel-wells d****s 1
    Committer Domains (Top 20 + Academic)
    roswellpark.org: 1 clemson.edu: 1

    Issues and Pull Requests

    Last synced: 11 months ago

    All Time
    • Total issues: 21
    • Total pull requests: 15
    • Average time to close issues: 6 minutes
    • Average time to close pull requests: about 2 months
    • Total issue authors: 11
    • Total pull request authors: 3
    • Average comments per issue: 1.43
    • Average comments per pull request: 0.4
    • Merged pull requests: 13
    • 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
    • brennanpincardiff (8)
    • janstrauss1 (3)
    • fifdick (2)
    • alptaciroglu (1)
    • shigekiiwase (1)
    • flubber-dom (1)
    • feudalab (1)
    • MauriAndresMU1313 (1)
    • MiguelCos (1)
    • geparada (1)
    • jmmelod (1)
    Pull Request Authors
    • brennanpincardiff (13)
    • daniel-wells (3)
    • stevin-wilson (1)
    Top Labels
    Issue Labels
    showcase drawProteins (1) help wanted (1) enhancement (1)
    Pull Request Labels

    Packages

    • Total packages: 1
    • Total downloads:
      • bioconductor 21,788 total
    • Total dependent packages: 1
    • Total dependent repositories: 0
    • Total versions: 6
    • Total maintainers: 1
    bioconductor.org: drawProteins

    Package to Draw Protein Schematics from Uniprot API output

    • Versions: 6
    • Dependent Packages: 1
    • Dependent Repositories: 0
    • Downloads: 21,788 Total
    Rankings
    Dependent repos count: 0.0%
    Dependent packages count: 0.0%
    Average: 16.9%
    Downloads: 50.6%
    Maintainers (1)
    brennanpincardiff@gmail.com
    Last synced: 11 months ago

    Dependencies

    DESCRIPTION cran
    • R >= 4.0 depends
    • dplyr * imports
    • ggplot2 * imports
    • httr * imports
    • readr * imports
    • tidyr * imports
    • BiocStyle * suggests
    • covr * suggests
    • knitr * suggests
    • rmarkdown * suggests
    • testthat * suggests