Metadata-Version: 2.1
Name: apafea
Version: 0.0.1
Summary: visualizes genes functional enrichment
Home-page: https://gitlab2.cip.ifi.lmu.de/puerckhauer/apafea
Author: Korbinian Pürckhauer
Author-email: korbinian@puerckhauer.net
Maintainer: Korbinian Pürckhauer
Maintainer-email: korbinian@puerckhauer.net
License: MIT
Download-URL: https://gitlab2.cip.ifi.lmu.de/puerckhauer/apafea
Project-URL: Bug tracker, https://gitlab2.cip.ifi.lmu.de/puerckhauer/apafea/-/issues
Keywords: gene,enrichment
Platform: UNKNOWN
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE.txt

# apafea

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    \ \  __ \  \ \  _-/ \ \  __ \  \ \  __\ \ \  __\   \ \  __ \  
     \ \_\ \_\  \ \_\    \ \_\ \_\  \ \_\    \ \_____\  \ \_\ \_\ 
      \/_/\/_/   \/_/     \/_/\/_/   \/_/     \/_____/   \/_/\/_/ 

* [Description](#description)
* [Installation](#installation)
* [Usage](#usage)
* [History](#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](#usage).
### Installation
Install the package with:
```pip install apafea```
### Usage
###### python:
```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


