GitHub - USCbiostats/HiLDA: :package: An R package for inferring the mutational exposures difference between groups. (original) (raw)

HiLDA: "_Hi_erarchical _L_atent _D_irichlet _A_llocation"

Introduction

The R package HiLDA is developed under the Bayesian framework to allow statistically testing whether there is a change in the mutation burdens of mutation signatures between two groups. The mutation signature is defined based on the independent model proposed by Shiraishi's et al.

Paper

• Yang Z, Pandey P, Shibata D, Conti DV, Marjoram P, Siegmund KD. 2019. HiLDA: a statistical approach to investigate differences in mutational signatures. PeerJ 7:e7557 https://doi.org/10.7717/peerj.7557

Installation

Now you can download the pacakge from Bioconductor https://bioconductor.org/packages/devel/bioc/html/HiLDA.html

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("HiLDA")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

An introduction to HiLDA

Tutorials:https://bioconductor.org/packages/devel/bioc/vignettes/HiLDA/inst/doc/HiLDA.html

R Scripts:https://bioconductor.org/packages/devel/bioc/vignettes/HiLDA/inst/doc/HiLDA.R

Funding

This work was supported by NCI grant numbers 5P30 CA014089 and P01 CA196569.