Data

Tools

Indexes

Applications

Experiments

Open Source Science

canprot

Chemical analysis of proteins

https://github.com/jedick/canprot

Science Score: 39.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 14 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.8%) to scientific vocabulary

Keywords

amino-acid-composition chemical-metrics hydration-state isoelectric-point oxidation-state proteins r
Last synced: 10 months ago · JSON representation

Repository

Chemical analysis of proteins

Basic Info
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 16
Topics
amino-acid-composition chemical-metrics hydration-state isoelectric-point oxidation-state proteins r
Created almost 10 years ago · Last pushed 12 months ago
Metadata Files
Readme License

README.md

CRAN/METACRAN Version R-CMD-check Codecov test coverage <!-- badges: end -->

canprot

Chemical analysis of proteins based on their amino acid compositions. Amino acid compositions can be read from FASTA files and used to calculate chemical metrics including carbon oxidation state and stoichiometric water content as described in Dick et al. (2020). Other properties that can be calculated include protein length, grand average of hydropathy (GRAVY), isoelectric point (pI), molecular weight (MW), standard molal volume (V0), and metabolic costs (Akashi and Gojobori, 2002; Wagner, 2005; Zhang et al., 2018). A database of amino acid compositions of human proteins derived from UniProt is provided.

See the vignettes at https://chnosz.net/canprot/vignettes/.

Installation

First install the remotes package from CRAN, then install canprot from GitHub. This also installs several other R packages as dependencies:

R install.packages("remotes") remotes::install_github("jedick/canprot")

Demo

Three demos are available. One of them is shown below.

```R demo("thermophiles")

demo("locations")

demo("redoxins")

```

Specific entropy and Zc and pI for Nitrososphaeria MAGs

This is a scatter plot of standard specific entropy (S° per gram) and carbon oxidation state (ZC) for proteins in Nitrososphaeria (syn. Thaumarchaeota) metagenome-assembled genomes (MAGs) reported by Luo et al. (2024). S° is calculated using amino acid group contributions (Dick et al, 2006) via canprot::S0g(). This plot reveals that proteins tend to have higher specific entropy in MAGs from thermal habitats compared to those from nonthermal habitats with similar carbon oxidation state. This implies that, after correcting for ZC, proteins in thermophiles have a more negative derivative of the standard Gibbs energy per gram of protein with respect to temperature. See the Demos for canprot vignette for a similar plot for genomes of methanogenic archaea.

Owner

  • Name: Jeffrey Dick
  • Login: jedick
  • Kind: user
  • Location: Changsha, China
  • Company: Central South University

Theoretical geochemist and developer of CHNOSZ.

GitHub Events

Total
  • Push event: 7
Last Year
  • Push event: 7

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 322
  • Total Committers: 1
  • Avg Commits per committer: 322.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 9
  • Committers: 1
  • Avg Commits per committer: 9.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
jedick j****k@g****m 322

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • 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
Pull Request Authors
  • jedick (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 358 last-month
  • Total docker downloads: 21,613
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 1
cran.r-project.org: canprot

Chemical Analysis of Proteins

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 358 Last month
  • Docker Downloads: 21,613
Rankings
Docker downloads count: 0.6%
Forks count: 21.0%
Average: 23.7%
Dependent repos count: 23.9%
Stargazers count: 25.5%
Dependent packages count: 28.7%
Downloads: 42.5%
Maintainers (1)
j3ffdick@gmail.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • CHNOSZ >= 1.3.2 depends
  • R >= 3.1.0 depends
  • MASS * imports
  • rmarkdown * imports
  • xtable * imports
  • knitr * suggests
  • testthat * suggests