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protGear

protGear is a package for protein microarray data processing just before the main analysis.

https://github.com/keniajin/protgear

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 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.2%) to scientific vocabulary

Keywords

background-correction microarray-data normalisation proteomics-data r shiny shinydashboard

Keywords from Contributors

bioconductor-package gene genomics sequencing ontology grna-sequence proteomics
Last synced: 6 months ago · JSON representation

Repository

protGear is a package for protein microarray data processing just before the main analysis.

Basic Info
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 4
  • Releases: 0
Topics
background-correction microarray-data normalisation proteomics-data r shiny shinydashboard
Created about 5 years ago · Last pushed about 3 years ago
Metadata Files
Readme

README.md

General information

protGear is a package for protein micro-array data processing just before the main analysis.

The package loads the 'gpr' or 'txt' file format extracted by the quantification software and merges this with the specific sample identifiers. The package processes multiple files extracted in a batch with their corresponding sample identifier file. The sample identifier file has 2 variables 'v1' and 'v2' which indicate the mini-array or block number and sample identifier respectively. The 'gpr' file and the corresponding sample identifier file have the same file name. protGear also provides a web based $Shiny^{(R)}$ platform for real time visualization of the data processing.

There is a package vignette included with this package with a step by step use of the package. Check https://keniajin.github.io/protGear/ under articles.

Installing the devel package

r library(remotes) remotes::install_github("keniajin/protGear")

Installing from Bioc BioConductor

``` r

install from BioConductor

if (!require("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("protGear") ```

To run the shiny application

To use the application locally on your compute install R and launch the app using the following command. protGear::launch_protGear_interactive()

To Install R: - Open an Internet browser and go to www.r-project.org. - Under "Getting Started" click the "download R" link - Select a CRAN location (a mirror site) and click the corresponding link. - Download R depending on your operating system.

protGear help pages

  • The main page - https://keniajin.github.io/protGear/
  • Vignette - https://keniajin.github.io/protGear/articles/vignette.html

Contribute

Check the Github page for source code.

Publication

Mwai K, Kibinge N, Tuju J, Kamuyu G, Kimathi R, Mburu J, Chepsat E, Nyamako L, Chege T, Nkumama I, Kinyanjui S. et al. , protGear: A protein microarray data pre-processing suite. Computational and Structural Biotechnology Journal. 2021 Apr 24.

DOI: https://doi.org/10.1016/j.csbj.2021.04.044

Owner

  • Name: Ken Mwai
  • Login: Keniajin
  • Kind: user
  • Location: Nairobi
  • Company: Keniajin Data Center

Data science | Bio-statistics | Data Visualization

GitHub Events

Total
Last Year

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 145
  • Total Committers: 5
  • Avg Commits per committer: 29.0
  • Development Distribution Score (DDS): 0.11
Past Year
  • Commits: 15
  • Committers: 2
  • Avg Commits per committer: 7.5
  • Development Distribution Score (DDS): 0.133
Top Committers
Name Email Commits
keniajin k****n@g****m 129
Ken Mwai K****n 9
Kennedy Mwai k****i@k****g 3
Nitesh Turaga n****a@g****m 2
J Wokaty j****y@s****u 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 kemri-wellcome.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 0
  • Average comments per issue: 1.25
  • 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
  • olferievm (2)
  • abiadak (1)
  • JosephLongworth (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 8,005 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: protGear

Protein Micro Array Data Management and Interactive Visualization

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 8,005 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 31.3%
Downloads: 93.8%
Maintainers (1)
keniajin@gmail.com
Last synced: 6 months ago