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:
GaMaBioMD_0.2.0.tar.gz
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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')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 11 months agofrom:8941f66a99. Checks:OK: 6 WARNING: 1. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 08 2024 |
R-4.5-win | OK | Oct 09 2024 |
R-4.5-linux | WARNING | Nov 08 2024 |
R-4.4-win | OK | Oct 09 2024 |
R-4.4-mac | OK | Oct 09 2024 |
R-4.3-win | OK | Oct 09 2024 |
R-4.3-mac | OK | Oct 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