Description: Tool for exploring DNA and amino acid variation and inferring the presence of target lineages from microbial high-throughput genomic DNA samples that potentially contain mixtures of variants/lineages. MixviR was originally created to help analyze environmental SARS-CoV-2/Covid-19 samples from environmental sources such as wastewater or dust, but can be applied to any microbial group. Inputs include reference genome information in commonly-used file formats (fasta, bed) and one or more variant call format (VCF) files, which can be generated with programs such as Illumina's DRAGEN, the Genome Analysis Toolkit, or bcftools. See DePristo et al (2011) <doi:10.1038/ng.806> and Danecek et al (2021) <doi:10.1093/gigascience/giab008> for these tools, respectively. Available outputs include a table of mutations observed in the sample(s), estimates of proportions of target lineages in the sample(s), and an R Shiny dashboard to interactively explore the data.

Title: Hyper Parameter Tuning for Machine Learning, Using Bayesian
Authors@R: person("Yuya", "Matsumura", email = "mattu.yuya@gmail.com",
Description: Hyper parameter tuning using Bayesian
optimization (Shahriari et al. <doi:10.1109/JPROC.2015.2494218>) for support vector machine,
random forest, and extreme gradient boosting (Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>).
Unlike already existing packages (e.g. 'mlr', 'rBayesianOptimization', or 'xgboost'), there is no need to change in accordance with the package or method of machine learning.
You just prepare a data frame with feature vectors and the label column that has any class ('character', 'factor', 'integer').
Moreover, to write a optimization function, you have only to specify the data and the column name of the label to classify.
Imports: xgboost(>= 0.6-4), Matrix, rBayesianOptimization(>= 1.1.0),
Suggests: MASS, testthat, knitr, rmarkdown

Packaged: 2019-03-20 07:04:30 UTC; matsumura

Title: Graphing for Markov, Hidden Markov, and Mixture Transition
Authors@R: c( person("Pauline (Poulcheria)", "Adamopoulou", role = c("aut",
"cre", "cph"), email = "padamopo@gmail.com"), person("Gilbert",
"Ritschard", role = c("ths"), email = "gilbert.ritschard@unige.ch"), person
("Andre", "Berchtold", role = c("ths"), email = "andre.berchtold@unil.ch"),
person ("Reto", "Buergin", role = c("ctb"), email = "rbuergin@gmx.ch"), person ("Ogier", "Maitre", role = c("ctb"), email = "ogier.maitre@epfl.ch"))
Maintainer: Pauline (Poulcheria) Adamopoulou <padamopo@gmail.com>
Description: Produces parallel coordinate plots of probability transition matrices from Markov, hidden Markov, and mixture transition distribution models.
Depends: R(>= 3.1.1), TraMineR, colorspace
Author: Pauline (Poulcheria) Adamopoulou [aut, cre, cph],