restez - Create and Query a Local Copy of 'GenBank' in R
Download large sections of 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local SQL-based database. A user can then query this database using 'restez' functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez> wrappers.
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dnaentrezgenbanksequence
6.40 score 28 stars 1 dependents 120 scripts 307 downloads
dwctaxon - Edit and Validate Darwin Core Taxon Data
Edit and validate taxonomic data in compliance with Darwin Core standards (Darwin Core 'Taxon' class <https://dwc.tdwg.org/terms/#taxon>).
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database
5.64 score 11 stars 354 downloads
canaper - Categorical Analysis of Neo- And Paleo-Endemism
Provides functions to analyze the spatial distribution of biodiversity, in particular categorical analysis of neo- and paleo-endemism (CANAPE) as described in Mishler et al (2014) <doi:10.1038/ncomms5473>. 'canaper' conducts statistical tests to determine the types of endemism that occur in a study area while accounting for the evolutionary relationships of species.
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biodiversitycanape
5.13 score 9 stars 372 downloadsrgnparser - Parse Scientific Names
Parse scientific names using 'gnparser' (<https://github.com/gnames/gnparser>), written in Go. 'gnparser' parses scientific names into their component parts; it utilizes a Parsing Expression Grammar specifically for scientific names.
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taxonomy
4.95 score 15 stars 1 dependents 301 downloads
taxastand - Taxonomic Name Standardization
Standardizes taxonomic names by matching species names to entries in a user-supplied reference taxonomy, then resolving synonyms to their accepted names. Fuzzy matching on parsed name components (genus, epithet, author, infraspecific rank, etc.) allows for orthographic differences between the query and reference names. This facilitates reproducible joining of datasets that use different taxonomic synonyms for the same species.
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databasetaxonomy
4.79 score 24 stars 17 scripts
citezot - Cite Zotero References in Quarto Documents
Scans Quarto and R Markdown documents for citation keys, pulls the matching items from the Zotero web API, and writes a bibliography file. Also provides dry-run-by-default helpers to find, add, and update Zotero items.
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bibilographyquartormarkdownzotero
3.11 score 13 scriptsftolr - Data for the Fern Tree of Life (FTOL)
Provides the Fern Tree of Life (FTOL) phylogeny and related data files.
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2.26 score 1 stars 18 scripts