Analysis of Short Tandem Repeat (STR) Massively Parallel
Sequencing (MPS) Data
Loading, identifying, aggregating, manipulating, and analysing short tandem repeat regions of massively parallel sequencing data in forensic genetics. 'STRMPS' can work with the package 'STRaitRazoR' (an R interface to the 'STRaitRazor' commandline tool) for added speed. 'STRaitRazoR' only works on linux and can found at <https://github.com/svilsen/STRaitRazoR>. The analyses and framework implemented in this package relies on the papers of Vilsen et al. (2017) <doi:10.1016/j.fsigen.2017.01.017> and Vilsen et al. (2018) <doi:10.1016/j.fsigen.2018.04.003>. Lastly, note that the parallelisation in the package relies on mclapply() and, thus, speed-ups will only be seen on UNIX based systems.
methods, utils, IRanges, tidyr, tibble, dplyr, stringr, purrr,
parallel

c(
person("John", "Emerson", email = "john.emerson@yale.edu", role = c("cre", "aut")),
person("Saksham", "Chandra", role = "aut"),
person("Lilla", "Orr", role = "aut"),
person("Efim", "Abrikosov", role = "ctb"),
person("Shadie", "Khubba", role = "ctb"),
person("William", "Meyerson", role = "ctb"),
person("Shylee", "Ezroni", role = "ctb"),
person("Junchao", "Ma", role = "ctb"))
Implementations of the Single Transferable Vote counting
system. By default, it uses the Cambridge method for surplus allocation
and Droop method for quota calculation.  Fractional surplus allocation
and the Hare quota are available as options.
John Emerson [cre, aut],
Saksham Chandra [aut],
Lilla Orr [aut],
Efim Abrikosov [ctb],
Shadie Khubba [ctb],
William Meyerson [ctb],
Shylee Ezroni [ctb],
Junchao Ma [ctb]

Enumeration and Uniform Sampling of Transmission Trees for a
Known Phylogeny
c(person("Matthew", "Hall", email = "matthew.hall@bdi.ox.ac.uk", role = c("aut", "cre")), person("Caroline", "Colijn", role = c("ctb")))
Matthew Hall [aut, cre],
Caroline Colijn [ctb]
For a single, known pathogen phylogeny, provides functions for enumeration of the set of compatible epidemic transmission trees, and for uniform sampling from that set. Optional arguments allow for incomplete sampling with a known number of missing individuals, multiple sampling, and known infection time limits. Always assumed are a complete transmission bottleneck and no superinfection or reinfection. See Hall and Colijn (2019) <doi:10.1093/molbev/msz058> for methodology.
ape, phangorn, igraph, gmp, ggplot2, ggtree (>= 1.14.6),
RcppAlgos, stats