Description: The SoundexBR package provides an algorithm for decoding names
into phonetic codes, as pronounced in Portuguese. The goal is for
homophones to be encoded to the same representation so that they can be
matched despite minor differences in spelling. The algorithm mainly encodes
consonants; a vowel will not be encoded unless it is the first letter. The
soundex code resultant consists of a four digits long string composed by
one letter followed by three numerical digits: the letter is the first
letter of the name, and the digits encode the remaining consonants.

Title: Single Cell mRNA Soup eXterminator
Maintainer: Matthew Daniel Young <my4@sanger.ac.uk>
Description: Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments.  Implements the method described in Young et al. (2018) <doi:10.1101/303727>.
Suggests: knitr, rstan, DropletUtils, rmarkdown
Imports: ggplot2, Matrix, methods, Seurat

Suggests: knitr, rstan, DropletUtils, rmarkdown, formatR

Imports: ggplot2, Matrix, methods, Seurat (>= 3.2.2)

Title: A Graphical Model Approach to Identify Primary Genes in
Authors@R: c(person("Elisa", "Salviato", email = "elisa.salviato.88@gmail.com", role = c("aut", "cre")),
person("Vera", "Djordjilovic", email = "vera.djordjilovic@medisin.uio.no", role = "aut"),
Description: The algorithm pursues the identification of the set of variables driving the differences in two different experimental conditions (i.e., the primary genes) within a graphical model context. It uses the idea of simultaneously looking for the differences between two multivariate normal distributions in all marginal and conditional distributions associated with a decomposable graph, which represents the pathway under exam. The implementation accommodates genomics specific issues (low sample size and multiple testing issues) and provides a number of functions offering numerical and visual summaries to help the user interpret the obtained results. In order to use the (optional) 'Cytoscape' functionalities, the suggested 'r2cytoscape' package must be installed from the 'GitHub' repository ('devtools::install_github('cytoscape/r2cytoscape')').
Imports: gRbase, progress, reshape2, graph, igraph, gtools, methods,
Suggests: networkD3, ggplot2, grDevices, Rgraphviz, knitr, rmarkdown,
r2cytoscape, BiocStyle, Biobase, graphite, hgu95av2.db, ALL,