Merge pull request #210 from CostaLab/develop

Develop

.gitignore

@@ -6,4 +6,5 @@ build/
 dist/
 docs/_build/
 .idea
-
+.vscode
+.DS_Store

.readthedocs.yml

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+version: 2
+build:
+  os: ubuntu-20.04
+  tools:
+    python: '3.8'
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt

README.md

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+[![Stars](https://img.shields.io/github/stars/CostaLab/reg-gen?logo=GitHub&color=yellow)](https://github.com/CostaLab/reg-gen/stargazers)
+[![PyPI](https://img.shields.io/pypi/v/rgt?logo=PyPI)](https://pypi.org/project/RGT/)
+[![PyPIDownloads](https://static.pepy.tech/badge/rgt)](https://static.pepy.tech/badge/rgt)
+[![Docs](https://readthedocs.org/projects/reg-gen/badge/?version=latest)](https://reg-gen.readthedocs.io)
+
+# RGT - Regulatory Genomics Toolbox
+
+RGT is an open source Python 3.6+ library for analysis of regulatory genomics. RGT is programmed in an oriented object fashion and its core classes provide functionality for handling regulatory genomics data.
+
+The toolbox is made of a core library and several tools:
+
+* [HINT](https://reg-gen.readthedocs.io/en/latest/hint/introduction.html): ATAC-seq/DNase-seq footprinting method
+* [THOR](https://reg-gen.readthedocs.io/en/latest/thor/introduction.html):
+ChIP-Seq differential peak caller
+* [Motif Analysis](https://reg-gen.readthedocs.io/en/latest/motif_analysis/introduction.html): TBFS match and enrichment
+* [RGT-Viz](https://reg-gen.readthedocs.io/en/latest/rgt-viz/introduction.html): Visualization tool
+* [TDF](https://reg-gen.readthedocs.io/en/latest/tdf/introduction.html): DNA/RNA triplex domain finder
+
+See https://reg-gen.readthedocs.io for documentation and tutorials.
+
+# Installation
+
+The quickest and easiest way to get RGT is to to use pip. First some dependencies:
+
+```shell
+pip install --user cython numpy scipy
+```
+
+Then install the full RGT suite with all other dependencies:
+```shell
+pip install --user RGT
+```
+
+Detailed installation instructions and basic problem solving can be found on our [website](https://reg-gen.readthedocs.io/en/latest/rgt/installation.html).
+