Title: Belief Propagation in Genotype-Phenotype Networks
Description: Belief propagation methods in genotype-phenotype networks (Conditional Gaussian Bayesian Networks) to propagate phenotypic evidence through the network.

Description: Belief propagation methods in genotype-phenotype networks (Conditional Gaussian and Discrete Bayesian Networks) to propagate phenotypic evidence through the network.

Title: Genome-Wide Association Study with SLOPE
Authors@R: c(person("Damian", "Brzyski", role = "aut"),
person("Christine", "Peterson", role = "aut"),
person("Piotr", "Sobczyk", email = "piotr.sobczyk@pwr.edu.pl", role = c("cre", "aut")))
Description: Genome-wide association study (GWAS) performed with SLOPE,
short for Sorted L-One Penalized Estimation, a
method for estimating the vector of coefficients in linear model.
In the first step of GWAS, SNPs are clumped according to their correlations and
distances. Then, SLOPE is performed on data where each clump has
Imports: ggplot2, bigmemory, grid, utils, stats
Suggests: shiny, knitr, rmarkdown, testthat

person("Emmanuel J.", "Candes", role = "aut"),

Author: Stefano M. Pagnotta, Michele Ceccarelli
Maintainer: Stefano M. Pagnotta <pagnotta@unisannio.it>
Description: A tool for finding an ensemble gene-signature by a
steepest ascending algorithm partially supervised by survival
Depends: survival, cluster, class, gplots, parallel, snow

Description: A tool for finding an ensemble gene-signature by a steepest ascending algorithm partially supervised by survival time data.
Depends: R (>= 3.0.0), survival, cluster, class, parallel

Title: Relevant Functions for Gene Expression Analysis, Especially in
Description: R package providing various functions relevant for gene
expression analysis with emphasis on breast cancer.
Author: Benjamin Haibe-Kains, Gianluca Bontempi, Christos Sotiriou
Depends: survcomp, amap, mclust, gplots, R (>= 2.5.0)

Author: Benjamin Haibe-Kains, Gianluca Bontempi, John Quackenbush,

Authors@R: c(person("Yunze", "Liu", email = "jieandze1314@gmail.com", role = c("aut", "cre")))
Description: An analysis toolkit based on gene. It mainly includes five
features (search, transform, analysis, visualization and export).
User just needs to provide gene id ('entrez', 'symbol' or 'ensembl') then can
search gene related information, transform id type, do enrichment analysis,
visualize enrichment result, visualized multi-group Venn diagram and export
result as excel sheets to easily share and communicate with others.
Imports: clusterProfiler, dplyr, ggplot2, stringr, stringi, tidyr,
Suggests: BiocManager, cowplot, DOSE, data.table, easyPubMed,
futile.logger, ggplotify, ggsci, ggupset, magrittr, msigdbr,
openxlsx, RColorBrewer, rentrez, scales, stats, utils