Package: agvgd 0.1.2
agvgd: An R Implementation of the 'Align-GVGD' Method
'Align-GVGD' ('A-GVGD') is a method to predict the impact of 'missense' substitutions based on the properties of amino acid side chains and protein multiple sequence alignments <doi:10.1136/jmg.2005.033878>. 'A-GVGD' is an extension of the original 'Grantham' distance to multiple sequence alignments. This package provides an alternative R implementation to the web version found on <http://agvgd.hci.utah.edu/>.
Authors:
agvgd_0.1.2.tar.gz
agvgd_0.1.2.zip(r-4.5)agvgd_0.1.2.zip(r-4.4)agvgd_0.1.2.zip(r-4.3)
agvgd_0.1.2.tgz(r-4.4-any)agvgd_0.1.2.tgz(r-4.3-any)
agvgd_0.1.2.tar.gz(r-4.5-noble)agvgd_0.1.2.tar.gz(r-4.4-noble)
agvgd_0.1.2.tgz(r-4.4-emscripten)agvgd_0.1.2.tgz(r-4.3-emscripten)
agvgd.pdf |agvgd.html✨
agvgd/json (API)
NEWS
# Install 'agvgd' in R: |
install.packages('agvgd', repos = c('https://maialab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/maialab/agvgd/issues
Last updated 9 months agofrom:4e746e319e. Checks:OK: 1 NOTE: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 14 2024 |
R-4.5-win | NOTE | Aug 14 2024 |
R-4.5-linux | NOTE | Aug 14 2024 |
R-4.4-win | NOTE | Aug 14 2024 |
R-4.4-mac | NOTE | Aug 14 2024 |
R-4.3-win | NOTE | Aug 14 2024 |
R-4.3-mac | NOTE | Aug 14 2024 |
Exports:%>%agvgdalignment_fileamino_acidscpv_rangesdevgdgvpoi_to_resprofile_to_alignmentread_agvgdweb_resultsread_alignmentread_substitutionsres_to_poiwrite_alignmentwrite_substitutions
Dependencies:ade4clicpp11crayondplyrfansigenericsgluegranthamlatticelifecyclemagrittrMASSnlmepillarpixmappkgconfigpurrrR6RcppRcppArmadillorlangsegmentedseqinrspstringistringrtibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Align-GVGD (A-GVGD) | agvgd |
Pre-bundled alignments | alignment_file |
The 20 standard amino acids | amino_acids |
Determine CPV ranges | cpv_ranges |
Deviation function | dev |
Grantham deviation | gd |
Grantham variation | gv |
Convert an alignment position to residue position | poi_to_res |
Converts a sequence profile to an alignment | profile_to_alignment |
Read a protein sequence multiple alignment | read_alignment |
Read a file with amino acid substitutions | read_substitutions |
Convert a residue position to an alignment position | res_to_poi |
Export an alignment to FASTA | write_alignment |
Generate and export a list of substitutions | write_substitutions |