GaMaBioMD: Diversity Analysis for Sequence Data

The full form is Garai and Mantri Biological Material Diversity. It is an R package designed for the calculation of biological diversity using sequence data. It simplifies the process by requiring only sample IDs and accession numbers. Whether you're analyzing genetic or microbial diversity, It provides efficient tools for diversity analysis. Serially one should go for the functions as presented here expand_accession_ranges(), get_sequence_information(), preprocess_for_alignment(), write_fasta(), SampleID_vs_NumSequences(), data_sampling(), alignment_info(), compute_average_similarity_matrix(), generate_heatmaps(), clustering_average_similarity(), clustering_percent_similarity(), bubble_plot_count(), bubble_plot_percentage(), tree_average_similarity(), tree_percent_similarity(). Till date there are total 15 functions. More details can be found in Faith (1992) <doi:10.1016/0006-3207(92)91201-3>.

Version: 0.2.0
Imports: traits, dplyr, magrittr, ggplot2, Biostrings, heatmaply, reshape2, dendextend, stats, ape
Published: 2024-01-12
Author: Sandip Garai [aut, cre], Shrikant Mantri [aut]
Maintainer: Sandip Garai <sandipnicksandy at gmail.com>
License: GPL-3
NeedsCompilation: no
CRAN checks: GaMaBioMD results

Documentation:

Reference manual: GaMaBioMD.pdf

Downloads:

Package source: GaMaBioMD_0.2.0.tar.gz
Windows binaries: r-devel: GaMaBioMD_0.2.0.zip, r-release: GaMaBioMD_0.2.0.zip, r-oldrel: GaMaBioMD_0.2.0.zip
macOS binaries: r-release (arm64): GaMaBioMD_0.2.0.tgz, r-oldrel (arm64): GaMaBioMD_0.2.0.tgz, r-release (x86_64): GaMaBioMD_0.2.0.tgz
Old sources: GaMaBioMD archive

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