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ropensci
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.
Maintained by Zachary Foster. Last updated 26 days ago.
taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize
274 stars 13.63 score 1.6k scripts 23 dependentsropensci
rotl:Interface to the 'Open Tree of Life' API
An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.
Maintained by Francois Michonneau. Last updated 2 years ago.
metadataropensciphylogeneticsindependant-contrastsbiodiversitypeer-reviewedphylogenytaxonomy
40 stars 12.05 score 356 scripts 29 dependentsropensci
taxa: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.
Maintained by Zachary Foster. Last updated 1 years ago.
taxonomybiologyhierarchydata-cleaningtaxon
47 stars 6.79 score 217 scripts
david-barnett
microViz:Microbiome Data Analysis and Visualization
Microbiome data visualization and statistics tools built upon phyloseq.
Maintained by David Barnett. Last updated 3 months ago.
microbiomemicrobiome-analysismicrobiota
114 stars 6.22 score 480 scripts