Metadata-Version: 2.1
Name: pysignora
Version: 0.1.1
Summary: Pathway gene-pair signature overrepresentation analysis
Home-page: https://github.com/veghp/pySignora
Author: Peter Vegh
License: GPLv3+
Description: # pySignora
        
        **pySignora** is a Python implementation of pathway gene-pair SIGnature OverRepresentation Analysis (SIGORA).
        
        SIGORA has been published in PeerJ and implemented in R (https://cran.r-project.org/web/packages/sigora/index.html) by *Foroushani et al.* (2013). Shortly, the method compiles a set of weighted markers, *pathway gene-pair signatures* (Pathway-GPS), for each pathway in a repository. Subsequently, it identifies statistically overrepresented Pathway-GPSs in a user-specified gene list, using an adapted version of the hypergeometric test.
        A *pathway* here is defined as a set of genes with the same pathway-ontology annotation. A pathway gene-pair signature is a pair of genes that, as a combination, are specific to a single pathway. The *weight* of a GPS expresses the average specificity of the two gene components towards the common pathway. The weight range is \[0, 1\].
        
        For more details, see the inventors' original publication: https://peerj.com/articles/229/
        
        The two core functions, GPS-generation and signature ORA, have been implemented, but the package is still **under development** and many important features will be added in the future:
        
        * Multiple-testing correction
        * KEGG, Reactome, GO and other databases
        * Handling hierarchical (multilevel) repositories
        
        
        ## Usage
        The input pandas dataframe (`repodf`) must have 3 columns: pathway, description, gene, e.g.:
        ```python
        import pandas as pd
        repodf[:3]
        #              pathwayId                           pathwayName             gene
        # 1  ecadherin_1_pathway           E-cadherin signaling events  ENSG00000168036
        # 2  ecadherin_1_pathway           E-cadherin signaling events  ENSG00000039068
        # 3   syndecan_2_pathway  Syndecan-2-mediated signaling events  ENSG00000101680
        ```
        
        ```python
        import pysignora as ps
        gps = ps.makegps(repodf)
        res = ps.signora(genelist, gps)
        ```
        
        
        ## Versioning
        
        pySignora uses the [semantic versioning](https://semver.org) scheme.
        
        
        ## License = GPLv3+
        
        pySignora is [free software](https://www.gnu.org/philosophy/free-sw.en.html), which means the users have the freedom to run, copy, distribute, study, change and improve the software.
        
        pySignora was written by [Peter Vegh](https://github.com/veghp) and is released under the GPLv3+ license.
        
Keywords: biology
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
