Package: canprot 2.0.0
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 hydration state, 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:
canprot_2.0.0.tar.gz
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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
amino-acid-compositionchemical-metricshydration-stateisoelectric-pointoxidation-stateproteins
Last updated 8 months agofrom:a824c02485. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 01 2024 |
| R-4.5-win | OK | Nov 01 2024 |
| R-4.5-linux | OK | Nov 01 2024 |
| R-4.4-win | OK | Nov 01 2024 |
| R-4.4-mac | OK | Nov 01 2024 |
| R-4.3-win | OK | Nov 01 2024 |
| R-4.3-mac | OK | Nov 01 2024 |
Exports:add_cldadd_hullB20Costcalc_metricscanprotCLESCostcount_aacplabDensityFermentativeCostGRAVYH11CostHChuman_aaMWnCNCnH2OnH2OgnO2nO2gOCpIplengthpMWpnCpS0pV0read_fastaRespiratoryCostS0S0gSCsum_aaSVV0V0gY20CostZcZcg
Dependencies:multcompViewstringi
Demos for canprot
Rendered fromdemos.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2024-03-28
Started: 2024-03-04
Introduction to canprot
Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2024-03-28
Started: 2024-02-29
More about metrics
Rendered frommetrics.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2024-03-03
Started: 2024-02-29
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Chemical analysis of proteins | canprot-package |
| Compact letter display | add_cld |
| Add convex hull | add_hull |
| Calculate one or more chemical metrics | calc_metrics |
| Common language effect size | CLES |
| Amino acid compositions of human proteins | canprot human human.aa human.additional human.base human.extra |
| Get amino acid compositions of human proteins | human_aa |
| Calculate chemical metrics for proteins | B20Cost 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 files | count_aa read_fasta sum_aa |
