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

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

Genome-Wide Association Study with SLOPE
c(person("Damian", "Brzyski", role = "aut"),
person("Christine", "Peterson", role = "aut"),
person("Malgorzata", "Bogdan", role = "aut"),
person("Chiara", "Sabatti", role = "aut"),
person("Piotr", "Sobczyk", email = "piotr.sobczyk@pwr.edu.pl", role = c("cre", "aut")))
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
one representative.
Damian Brzyski [aut],
Christine Peterson [aut],
Malgorzata Bogdan [aut],
Chiara Sabatti [aut],
Piotr Sobczyk [cre, aut]

c(person("Damian", "Brzyski", role = "aut"),
person("Christine", "Peterson", role = "aut"),
person("Emmanuel J.", "Candes", role = "aut"),
person("Malgorzata", "Bogdan", role = "aut"),
person("Chiara", "Sabatti", role = "aut"),
person("Piotr", "Sobczyk", email = "piotr.sobczyk@pwr.edu.pl", role = c("cre", "aut")))
Damian Brzyski [aut],
Christine Peterson [aut],
Emmanuel J. Candes [aut],
Malgorzata Bogdan [aut],
Chiara Sabatti [aut],
Piotr Sobczyk [cre, aut]

A tool for finding an ensemble gene-signature by a
steepest ascending algorithm partially supervised by survival
time data.
survival, cluster, class, gplots, parallel, snow

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

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