Metadata-Version: 2.1
Name: malachite
Version: 2.0.7
Summary: A Gene Enrichment Meta-Analysis (GEM) Tool for ToppGene
Home-page: https://github.com/ggersh/malachite-final
Author: Gregory R. Gershkowitz, Zachary B. Abrams, Kevin R. Coombes
Author-email: kevin.coombes@osumc.edu
License: UNKNOWN
Description: # Malachite: A Gene Enrichment Meta-Analysis (GEM) Tool for ToppGene
        
        Researchers commonly use software, such as Toppgene and online tools to conduct enrichment analyses on gene expression data. This process does not allow multiple gene data sets to be analyzed and compared at once. Malachite allows researchers to perform enrichment analyses on multiple gene lists and concatenate the resulting enrichment statistics, thus, enabling meta-enrichment analyses across multiple data sets.
        
        # How to Use:
        
        ## Command Line Argument Descriptions:
        
        #### 1. Full path to input file:
        
        ex. "/Desktop/myInput/input.xlsx"
        
        #### 2. Input type:
        ###### Choose one: HGNC, HGNC_SYNONYMS, ENTREZ, ENSEMBL, REFSEQ, UNIPROT
        
        ex. "HGNC"
        
        #### 3. Categories:
        ###### Options: "GeneOntologyMolecularFunction": "GO: Molecular Function", "GeneOntologyBiologicalProcess": "GO: Biological Process", "GeneOntologyCellularComponent":"GO: Cellular Component", "HumanPheno":"Human Phenotype","MousePheno":"Mouse Phenotype","Domain":"Domain", "Pathway":"Pathway","Pubmed":"Pubmed","Interaction":"Interaction","Cytoband":"Cytoband","TFBS":"Transcription Factor Binding Site","GeneFamily":"Gene Family","Coexpression":"Coexpression","CoexpressionAtlas":"Coexpression Atlas","Computational":"Computational","MicroRNA":"MicroRNA","Drug":"Drug","Disease":"Disease"
        
        ex. ["Drug", "Disease", "GeneOntologyMolecularFunction"]
        
        #### 4. Individual Toppgene analyses output path:
        
        ex. "/Desktop/Results/IndividualResults/"
        
        
        #### 5. Final Concatenated Results Output path:
        
        ex. "/Desktop/Results/ConcatenatedResults/"
        
        # For Example,
        
        ### In terminal type...
        
        malachite "/Desktop/myInput/input.xlsx" "HGNC" ["Drug", "Disease", "GeneOntologyMolecularFunction"] "/Desktop/Results/IndividualResults/" "/Desktop/Results/ConcatenatedResults/"
        
        ### *NOTE: quotation marks (“/‘) can be glitchy, make sure you use straight quotes, not curly quotes.
        ### *NOTE: input data has to be of type .xlsx
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
