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ropensci
beautier:'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.
Maintained by Richèl J.C. Bilderbeek. Last updated 1 months ago.
bayesianbeastbeast2beautiphylogenetic-inferencephylogenetics
13 stars 8.76 score 198 scripts 5 dependentsropensci
beastier: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.
Maintained by Richèl J.C. Bilderbeek. Last updated 1 months ago.
bayesianbeastbeast2phylogenetic-inferencephylogeneticsopenjdk
11 stars 7.87 score 47 scripts 4 dependents
richelbilderbeek
pureseqtmr:Predict Transmembrane Protein Topology
Proteins reside in either the cell plasma or in the cell membrane. A membrane protein goes through the membrane at least once. Given the amino acid sequence of a membrane protein, the tool 'PureseqTM' (<https://github.com/PureseqTM/pureseqTM_package>, as described in "Efficient And Accurate Prediction Of Transmembrane Topology From Amino acid sequence only.", Wang, Qing, et al (2019), <doi:10.1101/627307>), can predict the topology of a membrane protein. This package allows one to use 'PureseqTM' from R.
Maintained by Richèl J.C. Bilderbeek. Last updated 2 years ago.
1 stars 3.90 score 16 scriptsrichelbilderbeek
netmhc2pan:Interface to 'NetMHCIIpan'
The field of immunology benefits from software that can predict which peptide sequences trigger an immune response. 'NetMHCIIpan' is a such a tool: it predicts the binding strength of a short peptide to a Major Histocompatibility Complex class II (MHC-II) molecule. 'NetMHCIIpan' can be used from a web server at <https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/> or from the command-line, using a local installation. This package allows to call 'NetMHCIIpan' from R.
Maintained by Richèl J.C. Bilderbeek. Last updated 9 months ago.
1 stars 3.70 score 8 scripts