Package: sigora
Type: Package
Title: Signature Overrepresentation Analysis
Version: 3.0.5
Date: 2019-8-23
Author: Amir B.K. Foroushani, Fiona S.L. Brinkman, David J. Lynn
Maintainer: Amir Foroushani <sigora.dev@gmail.com>
Depends: R (>= 2.10)
Imports: utils,stats
Suggests: slam
Description: 
    Pathway Analysis is the process of statistically linking observations on 
    the molecular level to biological processes or pathways on the systems(i.e. 
     organism, organ, tissue, cell) level.  
    Traditionally, pathway analysis methods regard pathways as collections of 
    single genes and treat all genes in a pathway as equally informative. This 
    can lead to identification of spurious pathways as statistically significant,
    since components are often shared amongst pathways. 
    SIGORA seeks to avoid this pitfall by focusing on genes or gene-pairs 
    that are (as a combination) specific to a single pathway.  In relying on 
    such pathway gene-pair signatures (Pathway-GPS), SIGORA inherently uses 
    the status of other genes in the experimental context to identify the most 
    relevant pathways. 
    The current version allows for pathway analysis of human and mouse datasets 
    and contains pre-computed Pathway-GPS data for pathways in the KEGG and 
    Reactome pathway repositories as well as mechanisms for extracting GPS for 
    user supplied repositories.
License: GPL-2
LazyLoad: yes
LazyData: true
NeedsCompilation: no
Packaged: 2019-08-23 17:57:51 UTC; foroushaniak
Repository: CRAN
Date/Publication: 2019-08-23 18:20:02 UTC
Built: R 4.1.0; ; 2020-07-30 07:42:40 UTC; windows
