Author: Karl Kugler, Laurin Mueller, Simone Ecker, Armin Graber (with
performing meta-analysis. Note that from version 1.2 a complete
redesign of MADAM started to take place, so that code from
versions <1.2 will not be compatible with current versions.

Title: MHC Allele-Based Differencing Between Populations
Description: Tools for the analysis of population differences
using the Major Histocompatibility Complex (MHC) genotypes of samples
having a variable number of alleles (1-4) recorded for each
individual.  A hierarchical Dirichlet-Multinomial model on the
genotype counts is used to pool small samples from multiple
populations for pairwise tests of equality.  Bayesian inference is
implemented via the 'rstan' package.  Bootstrapped and posterior
p-values are provided for chi-squared and likelihood ratio tests of
Imports: methods, Rcpp (>= 0.12.0), stats, utils

Imports: methods, Rcpp (>= 0.12.0), stats

Authors@R: c(person("Martin", "Lysy", role = c("cre", "aut"),
person("Peter W.J.", "Kim", role = "aut"),
person("Terin", "Robinson", role = "ctb"))
Description: Tools for the analysis of population differences using the Major Histocompatibility Complex (MHC) genotypes of samples having a variable number of alleles (1-4) recorded for each individual.  A hierarchical Dirichlet-Multinomial model on the genotype counts is used to pool small samples from multiple populations for pairwise tests of equality.  Bayesian inference is implemented via the 'rstan' package.  Bootstrapped and posterior p-values are provided for chi-squared and likelihood ratio tests of equal genotype probabilities.
Imports: stats, utils, Rcpp (>= 0.12.9), methods (>= 3.3.2)

Title: Create an HTML Dashboard to Visualize Data from MAF File
person("Mayank", "Tandon", role = c("aut"), email = "mayank.tandon@nih.gov"),
person("Ashish", "Jain", role = c("aut", "cre"), email = "ashish.jain2@nih.gov"),
person("Frederick National Laboratory For Cancer Research", role = c("cph"))
Description: Mutation Annotation Format (MAF) is a tabular data format used for storing genetic mutation data.
For example, The Cancer Genome Atlas (TCGA) project has made MAF files from each project publicly available.
This package contains a set of tools to easily create an HTML dashboard to summarize and visualize data from MAF file.
The resulting HTML file serves as a self-contained report that can be used to explore the result.
Mayank Tandon & Ashish Jain (2020) <doi:10.5281/zenodo.4472978>.
Depends: R (>= 4.0.0), rmarkdown (>= 2.5.0), knitr (>= 1.3), htmltools
canvasXpress (>= 1.29.0), dplyr (>= 1.0.2), ComplexHeatmap (>=
ggbeeswarm (>= 0.6.0), ensurer (>= 1.1.0), data.table (>=
Frederick National Laboratory For Cancer Research [cph]