Package: canprot 2.0.0-7

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_2.0.0-7.tar.gz
canprot_2.0.0-7.zip(r-4.7-any)canprot_2.0.0-7.zip(r-4.6-any)canprot_2.0.0-7.zip(r-4.5-any)
canprot_2.0.0-7.tgz(r-4.6-any)canprot_2.0.0-7.tgz(r-4.5-any)
canprot_2.0.0-7.tar.gz(r-4.7-any)canprot_2.0.0-7.tar.gz(r-4.6-any)
canprot_2.0.0-7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
canprot/json (API)

# 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

6.00 score 4 stars 1 packages 55 scripts 443 downloads 1 mentions 41 exports 2 dependencies

Last updated from:ebf85c6831. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK137
source / vignettesOK197
linux-releaseOK135
macos-releaseOK144
macos-oldrelOK171
windows-develOK79
windows-releaseOK63
windows-oldrelOK70
wasm-releaseOK115

Exports:add_cldadd_hullB20Costcalc_metricscanprotCLESCostcount_aacplabDensityFermentativeCostGRAVYH11CostHChuman_aaMWnCNCnH2OnH2OgnO2nO2gOCpIplengthpMWpnCpS0pV0read_fastaRespiratoryCostS0S0gSCsum_aaSVV0V0gY20CostZcZcg

Dependencies:multcompViewstringi

Introduction to canprot
Reading FASTA files | Human proteins in canprot | References
Rendered fromintroduction.Rmdusingknitr::rmarkdown

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

More about metrics
More details on chemical metrics | Implementation details | GRAVY, pI, and molecular weight | References
Rendered frommetrics.Rmdusingknitr::rmarkdown

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

Demos for canprot
canprot demo #1: Thermophiles | canprot demo #2: Subcellular locations | canprot demo #3: Redoxins | References
Rendered fromdemos.Rmdusingknitr::rmarkdown

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

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