uyedaj/rphenoscate

Tools for analyzing trait evolution on phylogenetic trees with phenotypic ontologies

RPhenoscate: Semantics for Comparative Analyses of Trait Evolution

• Authors: Diego Porto, Sergei Tarasov, Caleb Charpentier, Hilmar Lapp, Josef Uyeda

• Maintainer: Josef Uyeda

• Install rphenoscape and rphenoscate packages using devtools:

install.packages("remotes")
require(remotes)
remotes::install_github("phenoscape/rphenoscape")
remotes::install_github("uyedaj/rphenoscate", build_vignettes = TRUE)

• Please report any bugs or issues at: https://github.com/uyedaj/rphenoscate/issues

• Tutorial and examples: https://github.com/diegosasso/rphenoscate_tutorials

• Manuscript describing package utilities: https://doi.org/XX.XXXX/XXX/XXX

• Additional information about the Phenoscape Project: https://phenoscape.org/ https://github.com/phenoscape

• Additional information about the SCATE Project: https://scate.phenoscape.org/

• Suggested literature:

1. [Balhoff et al. 2010] https://doi.org/10.1371/journal.pone.0010500
2. [Balhoff et al. 2014] http://dx.doi.org/10.1186/2041-1480-5-45
3. [Dececchi et al. 2015] https://doi.org/10.1093/sysbio/syv031
4. [Vogt 2017] https://doi.org/10.1111/cla.12209
5. [Vogt 2018] https://doi.org/10.1111/cla.12195
6. [Tarasov et al. 2019] https://doi.org/10.1093/isd/ixz009
7. [Tarasov 2019] https://doi.org/10.1093/sysbio/syz005
8. [Tarasov 2020] https://doi.org/10.1093/sysbio/syz050
9. [Tarasov 2022] https://doi.org/10.1101/2021.04.26.441495