Authors@R: c(person("Stefano", "Cacciatore", role = c("aut", "trl", "cre"),email = "tkcaccia@gmail.com", comment = c(ORCID = "0000-0001-7052-7156")),
person("Leonardo", "Tenori", role = "aut",email = "tenori@cerm.unifi.it", comment = c(ORCID = "0000-0001-6438-059X")))
Description: An unsupervised and semi-supervised learning algorithm that performs feature extraction
from noisy and high-dimensional data. It facilitates identification of patterns representing underlying
groups on all samples in a data set. Based on Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA.
(2017) Bioinformatics <doi:10.1093/bioinformatics/btw705> and Cacciatore S, Luchinat C, Tenori L. (2014)
Proc Natl Acad Sci USA <doi:10.1073/pnas.1220873111>.
Author: Stefano Cacciatore [aut, trl, cre]

Depends: R (>= 2.10.0), stats, minerva, Rtsne

Title: Functional Summary and Meta-Analysis of Gene Expression Data
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Description: Rank-based tests for enrichment of KOG (euKaryotic Orthologous Groups) classes with up- or down-regulated genes based on a continuous measure. The meta-analysis is based on correlation of KOG delta-ranks across datasets (delta-rank is the difference between mean rank of genes belonging to a KOG class and mean rank of all other genes). With binary measure (1 or 0 to indicate significant and non-significant genes), one-tailed Fisher's exact test for over-representation of each KOG class among significant genes will be performed.

Title: KONP Tests: Powerful K-Sample Tests for Right-Censored Data
Description: The K-sample omnibus non-proportional hazards (KONP) tests are powerful non-parametric tests for comparing K (>=2) hazard functions based on right-censored data (Gorfine, Schlesinger and Hsu, 2019, <arXiv:1901.05739v1>). These tests are consistent against any differences between the hazard functions of the groups. The KONP tests are often more powerful than other existing tests, especially under non-proportional hazard functions.
person("Matan", "Schlesinger", email = "matan.schles@gmail.com", role = c("cre","aut")),
person("Malka", "Gorfine", email = "gorfinem@tauex.tau.ac.il", role = "aut"))