babette - Control 'BEAST2'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an alternative workflow of using all these tools separately. This allows doing complex Bayesian phylogenetics easily and reproducibly from 'R'.
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bayesian-inferencebeast2phylogeneticsopenjdk
8.93 score 46 stars 1 dependents 70 scripts 395 downloadsbeautier - 'BEAUti' from R
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.
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bayesianbeastbeast2beautiphylogenetic-inferencephylogenetics
8.66 score 13 stars 5 dependents 222 scripts 497 downloadsbeastier - Call 'BEAST2'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.
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bayesianbeastbeast2phylogenetic-inferencephylogeneticsopenjdk
7.64 score 11 stars 4 dependents 55 scripts 438 downloadstracerer - Tracer from R
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'Tracer' (<https://github.com/beast-dev/tracer/>) is a GUI tool to parse and analyze the files generated by 'BEAST2'. This package provides a way to parse and analyze 'BEAST2' input files without active user input, but using R function calls instead.
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cpp
7.56 score 8 stars 3 dependents 85 scripts 360 downloadsmauricer - Work with 'BEAST2' Packages
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2' (<https://www.beast2.org>), which, among others, allows one to install 'BEAST2' package. This package allows to work with 'BEAST2' packages from 'R'.
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openjdk
5.55 score 3 stars 2 dependents 13 scripts 645 downloadsmcbette - Model Comparison Using 'babette'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'mcbette' allows to do a Bayesian model comparison over some site and clock models, using 'babette' (<https://github.com/ropensci/babette/>).
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openjdk
4.91 score 7 stars 23 scripts 290 downloadsmhcnuggetsr - Call MHCnuggets
MHCnuggets (<https://github.com/KarchinLab/mhcnuggets>) is a Python tool to predict MHC class I and MHC class II epitopes. This package allows one to call MHCnuggets from R.
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4.48 score 4 stars 15 scripts 233 downloads