Package: GaMaBioMD 0.2.0

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>.

Authors:Sandip Garai [aut, cre], Shrikant Mantri [aut]

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GaMaBioMD.pdf |GaMaBioMD.html
GaMaBioMD/json (API)

# Install 'GaMaBioMD' in R:
install.packages('GaMaBioMD', repos = c('https://sandipgarai.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

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

1.00 score 199 downloads 15 exports 156 dependencies

Last updated 10 months agofrom:8941f66a99. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 09 2024
R-4.5-winOKOct 09 2024
R-4.5-linuxOKOct 09 2024
R-4.4-winOKOct 09 2024
R-4.4-macOKOct 09 2024
R-4.3-winOKOct 09 2024
R-4.3-macOKOct 09 2024

Exports:alignment_infobubble_plot_countbubble_plot_percentageclustering_average_similarityclustering_percent_similaritycompute_average_similarity_matrixdata_samplingexpand_accession_rangesgenerate_heatmapsget_sequence_informationpreprocess_for_alignmentSampleID_vs_NumSequencestree_average_similaritytree_percent_similaritywrite_fasta

Dependencies:apeaskpassassertthatbackportsbase64encBiocGenericsBiostringsbitbit64bslibcacachemcallrcheckmateclicliprclustercodetoolscolorspaceconditionzcpp11crayoncrosstalkcrulcurldata.tabledendextenddigestdplyreggevaluatefansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsgclusgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegridExtragtableheatmaplyhighrHmischmshoardrhtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnatservnlmennetopensslpbapplypermutephangornpillarpkgconfigplotlyplyrprettyunitsprocessxprogresspromisespspurrrqapquadprogR6rappdirsratelimitrRColorBrewerRcppreadrregistryrentrezreshape2rexritisrlangrmarkdownrnclrotlrpartrredlistrstudioapirvestS4VectorssassscalesselectrseriationsolriumstringistringrsystaxizetibbletidyrtidyselecttinytextraitstriebeardTSPtzdbUCSC.utilsurltoolsutf8uuidvctrsveganviridisviridisLitevroomwebshotWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2XVectoryamlzlibbioczoo