apafea 0.0.3

visualizes genes functional enrichment

apafea

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• Description
• Installation
• Usage
• History

Description

apafea is short for "alluvial plots as functional enrichment analysis".
And it does just that. Input a set of gene clusters (supports KeyPathwayMiner & BiCoN) and apafea performs gene set enrichment analysis and shows an alluvial plot visualizing the results.
For further Information check out usage.

Installation

Install the package with: pip install apafea

Usage

python:

from apafea import run

run(
    mode="KPM",
    data="/absolute/path/to/directory/",
    mode_2="BiCoN",
    data_2="/absolute/path/to/results.csv",
    gsea_dir="/absolute/path/to/gsea/directory/",
    GO=["bp",
        "cc",
        "mf",
        "pw"],
    PW=["KEGG",
        "Reactome",
        "WikiPathways",
        "MSigDB_C",
        "MSigDB_O_S"],
    all=False,
    cutoff=0.05,
)

explanation:

• "mode" - defines the type of input.
  • "KPM" - give the path to your KeyPythwayMiner output directory under "data"
  • "BiCoN" - give the path to your BiCoN result .csv file under "data"
  • "custom" - give the path to your directory under "data" containing 1 cluster per file like this:

  gene1
  gene2
  ...
  

• "mode_2" - defines the type of input for cluster comparison analysis.
  • "KPM" - same as above
  • "BiCoN" - same as above
  • "custom" - same as above
  • None / not set - cluster comparison analysis will not be performed

• "gsea_dir" - give the path to a directory to be used as gene set enrichment analysis output directory (default: /tmp)
• "GO" - list of GO-Terms enrichment analysis is being performed for
  • "bp" - Biological process
  • "cc" - Cellular Component
  • "mf" - molecular Function
  • "pw" - KEGG Pathways
  • None / [] / not set - analysis will not be performed
• "PW" - list of pathway databases enrichment analysis is being performed for
  • "KEGG" - KEGG_2016
  • "Reactome" - Reactome_2016
  • "WikiPathways" - WikiPathways_2016
  • "MSigDB_C" - MSigDB_Computational
  • "MSigDB_O_S" - MSigDB_Oncogenic_Signatures
  • None / [] / not set - analysis will not be performed
• "all" - associates all its terms to a gene (default: False)
• "cutoff" - defines the cutoff for gene set enrichment analysis (default: 0.05)

History

• 0.0.0 - initial commit
• 0.0.1 - first official release
• 0.0.2 - added MANIFEST.in and changed relative path handling for sample data
• 0.0.3 - fixed bug with relative path handling for sample data