Package: bios2mds 1.2.3

Marie Chabbert

bios2mds: From Biological Sequences to Multidimensional Scaling

Utilities dedicated to the analysis of biological sequences by metric MultiDimensional Scaling with projection of supplementary data. It contains functions for reading multiple sequence alignment files, calculating distance matrices, performing metric multidimensional scaling and visualizing results.

Authors:Julien Pele with Jean-Michel Becu, Rym Ben Boubaker, Herve Abdi, and Marie Chabbert

bios2mds_1.2.3.tar.gz
bios2mds_1.2.3.tar.gz(r-4.5-noble)bios2mds_1.2.3.tar.gz(r-4.4-noble)
bios2mds_1.2.3.tgz(r-4.4-emscripten)bios2mds_1.2.3.tgz(r-4.3-emscripten)
bios2mds.pdf |bios2mds.html✨
bios2mds/json (API)

# Install 'bios2mds' in R:

install.packages('bios2mds', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

gpcr - Pre-analyzed G-Protein-Coupled Receptor (GPCR) data set
sub.mat - Amino acid substitution matrices

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.90 score 1 stars 272 downloads 8 mentions 20 exports 42 dependencies

Last updated 5 years agofrom:af41d2a3de. Checks:1 OK, 1 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 06 2025
R-4.5-linux	NOTE	Feb 06 2025

Exports:col.group dif dis export.fasta extract.cluster import.fasta import.msf kmeans.run mat.dif mat.dis mmds mmds.2D.multi mmds.2D.plot mmds.3D.plot mmds.plot mmds.project random.msa scree.plot sil.score write.mmds.pdb

Dependencies:amap base64enc bslib cachem class cli cluster colorspace digest e1071 evaluate farver fastmap fontawesome fs glue highr htmltools htmlwidgets jquerylib jsonlite knitr labeling lifecycle magrittr MASS memoise mime munsell proxy R6 rappdirs RColorBrewer rgl rlang rmarkdown sass scales tinytex viridisLite xfun yaml

Citation

Readme and manuals

Help Manual

Help page	Topics
From BIOlogical Sequences to MultiDimensional Scaling	bios2mds-package bios2mds
Links elements in a mmds object to specific groups and colors	col.group
Difference score	dif
Dissimilarity score	dis
Writes a MSA file in FASTA format	export.fasta
Extraction of clusters alignments	extract.cluster
Pre-analyzed G-Protein-Coupled Receptor (GPCR) data set	gpcr
Reads a file in FASTA format	import.fasta
Reads a multiple sequence alignment file in MSF format	import.msf
Multiple runs of K-means analysis	kmeans.run
Matrices of difference scores between sequences	mat.dif
Matrices of dissimilarity scores between amino acid sequences	mat.dis
Metric multidimensional scaling	mmds
Plots the mmds coordinates onto a 2D space	mmds.2D.multi
Plots the mmds coordinates onto a 2D space	mmds.2D.plot
Display the mmds coordinates onto a 3D space	mmds.3D.plot
Plots a summary of the mmds results	mmds.plot
Metric multidimensional Scaling Projection	mmds.project
Random Alignment	random.msa
Plots the eingenvalues of an MDS analysis	scree.plot
Silhouette score	sil.score
Amino acid substitution matrices	sub.mat
Writes PDB file	write.mmds.pdb

Package: bios2mds 1.2.3

bios2mds: From Biological Sequences to Multidimensional Scaling

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)