Metadata-Version: 2.1
Name: scircm
Version: 1.0.1
Summary: UNKNOWN
Home-page: https://github.com/ArianeMora/scircm
Author: Ariane Mora
Author-email: ariane.n.mora@gmail.com
License: GPL3
Project-URL: Bug Tracker, https://github.com/ArianeMora/scircm/issues
Project-URL: Documentation, https://github.com/ArianeMora/scircm
Project-URL: Source Code, https://github.com/ArianeMora/scircm
Keywords: epigenetics,bioinformatics
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: scibiomart
Requires-Dist: sciutil (>=1.0.3)
Requires-Dist: scivae
Requires-Dist: sklearn
Requires-Dist: sciviso
Requires-Dist: seaborn
Requires-Dist: stats
Requires-Dist: matplotlib-venn
Requires-Dist: scimotf
Requires-Dist: scie2g

# sci-RegulatoryClusteringModel
[![codecov.io](https://codecov.io/github/ArianeMora/scircm/coverage.svg?branch=master)](https://codecov.io/github/ArianeMora/scircm?branch=master)
[![PyPI](https://img.shields.io/pypi/v/scircm)](https://pypi.org/project/scircm/)
[![DOI](https://zenodo.org/badge/316410924.svg)](https://zenodo.org/badge/latestdoi/316410924)

[Link to docs](https://arianemora.github.io/scircm/)

## Regulatory clustering model 

The general table of how we define regulatory clusters.

| Methylation      | RNAseq    | Proteomics | Regulation driver_1          | Regulation driver_2     | Regulation_Grouping1 | Regulation_Grouping2 | Regulation_Grouping3 |
|------------------|-----------|------------|------------------------------|-------------------------|----------------------|----------------------|----------------------|
| Hypermethylation | DOWN      | DOWN       | Methylation increase (MDS)   | None                    | MDS                  | MDS                  | MDS                  |
| Hypermethylation | UP        | DOWN       | mRNA increase (TPDE)         | Protein decrease (TMDS) | TPDE+TMDS            | TPDE+TMDS            | TMDS                 |
| Hypermethylation | UP        | UP         | mRNA increase (TPDE)         | None                    | TPDE                 | TPDE                 | TPDE                 |
| Hypermethylation | DOWN      | UP         | Methylation increase (MDS)   | Protein increase (TMDE) | MDS+TMDE             | TMDE                 | TMDE                 |
| Hypermethylation | No Change | UP         | mRNA increase (TPDE)         | Protein increase (TMDE) | TPDE+TMDE            | TMDE                 | TMDE                 |
| Hypermethylation | No Change | DOWN       | mRNA increase (TPDE)         | Protein decrease (TMDS) | TPDE+TMDS            | TMDS                 | TMDS                 |
| Hypermethylation | UP        | No Change  | mRNA increase (TPDE)         | Protein decrease (TMDS) | TPDE+TMDS            | TPDE+TMDS            | TMDS                 |
| Hypermethylation | DOWN      | No Change  | Methylation increase (MDS)   | Protein increase (TMDE) | MDS+TMDE             | MDS+TMDE             | TMDE                 |
| Hypermethylation | No Change | No Change  | Methylation increase (ncRNA) | None                    | MDS-ncRNA            | MDS_ncRNA            | MDS_ncRNA            |
| Hypomethylation  | DOWN      | DOWN       | mRNA decrease (TPDS)         | None                    | TPDS                 | TPDS                 | TPDS                 |
| Hypomethylation  | UP        | DOWN       | Methylation decrease (MDE)   | Protein decrease (TMDS) | MDE+TMDS             | TMDS                 | TMDS                 |
| Hypomethylation  | UP        | UP         | Methylation decrease (MDE)   | None                    | MDE                  | MDE                  | MDE                  |
| Hypomethylation  | DOWN      | UP         | mRNA decrease (TPDS)         | Protein increase (TMDE) | TPDS+TMDE            | TPDS+TMDE            | TMDE                 |
| Hypomethylation  | No Change | UP         | mRNA decrease (TPDS)         | Protein increase (TMDE) | TPDS+TMDE            | TMDE                 | TMDE                 |
| Hypomethylation  | No Change | DOWN       | mRNA decrease (TPDS)         | Protein decrease (TMDS) | TPDS+TMDS            | TMDS                 | TMDS                 |
| Hypomethylation  | UP        | No Change  | Methylation decrease (MDE)   | Protein decrease (TMDS) | MDE+TMDS             | MDE+TMDS             | TMDS                 |
| Hypomethylation  | DOWN      | No Change  | mRNA decrease (TPDS)         | Protein increase (TMDE) | TPDS+TMDE            | TPDS+TMDE            | TMDE                 |
| Hypomethylation  | No Change | No Change  | Methylation decrease (ncRNA) | None                    | MDE+ncRNA            | MDE_ncRNA            | MDE_ncRNA            |
| No Change        | DOWN      | UP         | mRNA decrease (TPDS)         | Protein increase (TMDE) | TPDS+TMDE            | TPDS+TMDE            | TMDE                 |
| No Change        | UP        | DOWN       | mRNA increase (TPDE)         | Protein decrease (TMDS) | TPDE+TMDS            | TPDE+TMDS            | TMDS                 |
| No Change        | DOWN      | DOWN       | mRNA decrease (TPDS)         | None                    | TPDS                 | TPDS                 | TPDS                 |
| No Change        | UP        | UP         | mRNA increase (TPDE)         | None                    | TPDE                 | TPDE                 | TPDE                 |
| No Change        | No Change | UP         | Protein increase (TMDE)      | None                    | TMDE                 | TMDE                 | TMDE                 |
| No Change        | No Change | DOWN       | Protein decrease (TMDS)      | None                    | TMDS                 | TMDS                 | TMDS                 |
| No Change        | UP        | No Change  | mRNA increase (TPDE)         | Protein decrease (TMDS) | TPDE+TMDS            | TPDE+TMDS            | TMDS                 |
| No Change        | DOWN      | No Change  | mRNA decrease (TPDS)         | Protein increase (TMDE) | TPDS+TMDE            | TPDS+TMDE            | TMDE                 |
| No Change        | No Change | No Change  | NoChange                     | NoChange                | NoChange             | NoChange             | NoChange             |

Please post questions and issues related to sci-rcm on the `Issues <https://github.com/ArianeMora/scircm/issues>`_  section of the GitHub repository.



