knitr, ggplot2, leaflet, mapdeck, rmarkdown, readr, rgdal,
rgeos, scales, sp, sf, geojsonsf, tidyr, lwgeom

Integrated, convenient, and uniform access to Canadian
Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready
tidy data frames and spatial data in multiple formats, as well as convenience functions
for working with Census variables, variable hierarchies, and region selection. API
keys are freely available with free registration at <https://censusmapper.ca/api>.
Census data and boundary geometries are reproduced and distributed on an "as
is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006;
2011; 2016; 2021).

Functions to perform the following analyses: i) inferring epistasis from RNAi double knockdown data; ii) identifying gene pairs of multiple mutation patterns; iii) assessing association between gene pairs and survival; and iv) calculating the smallworldness of a graph (e.g., a gene interaction network).  Data and analyses are described in Wang, X., Fu, A. Q., McNerney, M. and White, K. P. (2014). Widespread genetic epistasis among breast cancer genes. Nature Communications. 5 4828. <doi:10.1038/ncomms5828>.
systemfit, qvalue, survival, reshape2, igraph

Estimation of temporal ordering of cancer abnormalities
This is a package with functions for timing copy number
changes using estimates of mutational allele frequency from
resequencing of tumor samples.
R (>= 2.11.0), LearnBayes, GenomicRanges

This is a package with functions for timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.

Estimation of Temporal Ordering of Cancer Abnormalities

utils, stats, grDevices, graphics, LearnBayes, gplots

Timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.

Functions for computing and graphing canonical discriminant
analyses.

car, heplots (>= 0.8-3), graphics, stats

Functions for computing and graphing canonical
discriminant analyses.