Package: canprot 2.0.0-5

canprot: Chemical Analysis of Proteins

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) <doi:10.5194/bg-17-6145-2020>. 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 <doi:10.1073/pnas.062526999>; Wagner, 2005 <doi:10.1093/molbev/msi126>; Zhang et al., 2018 <doi:10.1038/s41467-018-06461-1>). A database of amino acid compositions of human proteins derived from UniProt is provided.

Authors:Jeffrey Dick [aut, cre]

canprot_2.0.0-5.tar.gz
canprot_2.0.0-5.zip(r-4.5)canprot_2.0.0-5.zip(r-4.4)canprot_2.0.0-5.zip(r-4.3)
canprot_2.0.0-5.tgz(r-4.5-any)canprot_2.0.0-5.tgz(r-4.4-any)canprot_2.0.0-5.tgz(r-4.3-any)
canprot_2.0.0-5.tar.gz(r-4.5-noble)canprot_2.0.0-5.tar.gz(r-4.4-noble)
canprot_2.0.0-5.tgz(r-4.4-emscripten)canprot_2.0.0-5.tgz(r-4.3-emscripten)
canprot.pdf |canprot.html
canprot/json (API)
NEWS

# Install 'canprot' in R:
install.packages('canprot', repos = c('https://jedick.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jedick/canprot/issues

On CRAN:

Conda:

amino-acid-compositionchemical-metricshydration-stateisoelectric-pointoxidation-stateproteins

6.64 score 3 stars 1 packages 46 scripts 330 downloads 1 mentions 41 exports 2 dependencies

Last updated 6 days agofrom:c6e6bd22ce. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 24 2025
R-4.5-winOKMar 24 2025
R-4.5-macOKMar 24 2025
R-4.5-linuxOKMar 24 2025
R-4.4-winOKMar 24 2025
R-4.4-macOKMar 24 2025
R-4.4-linuxOKMar 24 2025
R-4.3-winOKMar 24 2025
R-4.3-macOKMar 24 2025

Exports:add_cldadd_hullB20Costcalc_metricscanprotCLESCostcount_aacplabDensityFermentativeCostGRAVYH11CostHChuman_aaMWnCNCnH2OnH2OgnO2nO2gOCpIplengthpMWpnCpS0pV0read_fastaRespiratoryCostS0S0gSCsum_aaSVV0V0gY20CostZcZcg

Dependencies:multcompViewstringi

Demos for canprot

Rendered fromdemos.Rmdusingknitr::rmarkdownon Mar 24 2025.

Last update: 2024-03-28
Started: 2024-03-04

Introduction to canprot

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Mar 24 2025.

Last update: 2024-12-09
Started: 2024-02-29

More about metrics

Rendered frommetrics.Rmdusingknitr::rmarkdownon Mar 24 2025.

Last update: 2024-12-09
Started: 2024-02-29

Readme and manuals

Help Manual

Help pageTopics
Chemical analysis of proteinscanprot-package
Compact letter displayadd_cld
Add convex hulladd_hull
Calculate one or more chemical metricscalc_metrics
Common language effect sizeCLES
Amino acid compositions of human proteinscanprot human human.aa human.additional human.base human.extra
Get amino acid compositions of human proteinshuman_aa
Calculate chemical metrics for proteinsB20Cost Cost cplab Density FermentativeCost GRAVY H11Cost HC metrics MW NC nC nH2O nH2Og nO2 nO2g OC pI plength pMW pnC pS0 pV0 RespiratoryCost S0 S0g SC SV V0 V0g Y20Cost Zc Zcg
Functions for reading FASTA filescount_aa read_fasta sum_aa