taxize - Taxonomic Information from Around the Web
Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.
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taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize
10.61 score 303 stars 14 dependents 2 scripts 4.7k downloadsmetacoder - Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data
Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) <doi:10.1371/journal.pcbi.1005404>.
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community-diversityhierarchicalmetabarcodingpcrtaxonomytreescpp
9.77 score 147 stars 383 scripts 953 downloadswikitaxa - Taxonomic Information from 'Wikipedia'
'Taxonomic' information from 'Wikipedia', 'Wikicommons', 'Wikispecies', and 'Wikidata'. Functions included for getting taxonomic information from each of the sources just listed, as well performing taxonomic search.
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taxonomyspeciesapiweb-serviceswikipediavernacularwikispecieswikicommonstaxizewikipedia-api
7.75 score 22 stars 15 dependents 3.8k downloadstaxa - Classes for Storing and Manipulating Taxonomic Data
Provides classes for storing and manipulating taxonomic data. Most of the classes can be treated like base R vectors (e.g. can be used in tables as columns and can be named). Vectorized classes can store taxon names and authorities, taxon IDs from databases, taxon ranks, and other types of information. More complex classes are provided to store taxonomic trees and user-defined data associated with them.
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taxonomybiologyhierarchydata-cleaningtaxon
5.49 score 51 stars 470 downloadsheattree - A Self-Contained Widget for Interactive Phylogenetic Tree Visualization
Creates self-contained widgets for interactive phylogenetic tree visualization. This package wraps the 'JavaScript' 'heat-tree' package using the 'htmlwidgets' R package.
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4.41 score 4 stars 6 scripts 244 downloads