Package: grantham 0.1.1
grantham: Calculate the 'Grantham' Distance
A minimal set of routines to calculate the 'Grantham' distance <doi:10.1126/science.185.4154.862>. The 'Grantham' distance attempts to provide a proxy for the evolutionary distance between two amino acids based on three key chemical properties: composition, polarity and molecular volume. In turn, evolutionary distance is used as a proxy for the impact of missense mutations. The higher the distance, the more deleterious the substitution is expected to be.
Authors:
grantham_0.1.1.tar.gz
grantham_0.1.1.zip(r-4.5)grantham_0.1.1.zip(r-4.4)grantham_0.1.1.zip(r-4.3)
grantham_0.1.1.tgz(r-4.4-any)grantham_0.1.1.tgz(r-4.3-any)
grantham_0.1.1.tar.gz(r-4.5-noble)grantham_0.1.1.tar.gz(r-4.4-noble)
grantham_0.1.1.tgz(r-4.4-emscripten)grantham_0.1.1.tgz(r-4.3-emscripten)
grantham.pdf |grantham.html✨
grantham/json (API)
NEWS
# Install 'grantham' in R: |
install.packages('grantham', repos = c('https://ramiromagno.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/maialab/grantham/issues
- amino_acids_properties - Amino acid side chain property values
- grantham_distances_matrix - Grantham distance matrix
Last updated 1 months agofrom:6768b1f580. Checks:OK: 7. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 02 2024 |
R-4.5-win | OK | Sep 02 2024 |
R-4.5-linux | OK | Sep 02 2024 |
R-4.4-win | OK | Sep 02 2024 |
R-4.4-mac | OK | Sep 02 2024 |
R-4.3-win | OK | Sep 02 2024 |
R-4.3-mac | OK | Sep 02 2024 |
Exports:%>%amino_acid_pairsamino_acidsas_one_letteras_three_lettergrantham_distancegrantham_distance_exactgrantham_distance_originalgrantham_equation
Dependencies:clicpp11dplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Generate amino acid pairs | amino_acid_pairs |
The 20 standard amino acids | amino_acids |
Amino acid side chain property values | amino_acids_properties |
Convert three-letter amino acid codes to one-letter codes | as_one_letter |
Convert one-letter amino acid codes to three-letter codes | as_three_letter |
Grantham distance | grantham_distance |
Grantham distance matrix | grantham_distances_matrix |
Grantham distance | grantham_equation |