Merge pull request #11 from a-slide/dev

Dev

README.md

@@ -4,7 +4,6 @@
 [![Language](https://img.shields.io/badge/Language-Python3-yellow.svg)](https://www.python.org/)
 [![PyPI version](https://badge.fury.io/py/pycoMeth.svg)](https://badge.fury.io/py/pycoMeth)
 [![PyPI downloads](https://pepy.tech/badge/pycoMeth)](https://pepy.tech/project/pycoMeth)
-
 <!-- [![DOI](https://zenodo.org/badge/144169864.svg)](https://zenodo.org/badge/latestdoi/144169864) -->
 
 ---
@@ -13,9 +12,13 @@
 
 ---
 
-**Python package for nanopore DNA methylation analysis downstream to Nanopolish**
+**DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets**
+
+`pycoMeth` can be used for further analyses starting from the output files generated by [`Nanopolish call-methylation`](https://github.com/jts/nanopolish). The package contains a suite of tools to **find CpG islands** calculate the **methylation probability at CpG dinucleotide or CpG island resolution** across the entire genome and to perform a **simple differential methylation analysis** across multiple samples.
+
+`pycoMeth` generates extensive tabulated reports and BED files which can be loaded in a genome browser. However, this is not a visualisation tool *per se*. An excellent complementary tool to visualise and explore methylation status for specific loci is [`Methplotlib`](https://github.com/wdecoster/methplotlib) developed by [Wouter de coster](https://twitter.com/wouter_decoster).
 
-`pycoMeth` can be used for further analysis starting from the output files generated by [`Nanopolish call-methylation`](https://github.com/jts/nanopolish). The package contains tools to **summarize the methylation data at CpG or CpG island resolution** .`pycoMeth` also includes a simple method for **differential methylation analysis** across multiple samples.
+Please be aware that `pycoMeth` is a research package that is still under development. The API, command line interface, and implementation might change without retro-compatibility.
 
 ---
 

docs/index.md

@@ -1,10 +1,18 @@
-![](./pictures/pycoMeth_long.png)
+![](./docs/pictures/pycoMeth_long.png)
+
+[![GitHub license](https://img.shields.io/github/license/a-slide/pycoMeth.svg)](https://github.com/a-slide/pycoMeth/blob/master/LICENSE)
+[![Language](https://img.shields.io/badge/Language-Python3-yellow.svg)](https://www.python.org/)
+[![PyPI version](https://badge.fury.io/py/pycoMeth.svg)](https://badge.fury.io/py/pycoMeth)
+[![PyPI downloads](https://pepy.tech/badge/pycoMeth)](https://pepy.tech/project/pycoMeth)
+<!-- [![DOI](https://zenodo.org/badge/144169864.svg)](https://zenodo.org/badge/latestdoi/144169864) -->
 
 # Welcome to pycoMeth documentation
 
-**Python package for nanopore DNA methylation analysis downstream to Nanopolish**
+---
+
+**DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets**
 
-`pycoMeth` can be used for further analysis starting from the output files generated by [`Nanopolish call-methylation`](https://github.com/jts/nanopolish). The package contains tools to **summarize the methylation data at CpG or CpG island resolution**. `pycoMeth` also includes a simple method for **differential methylation analysis** across multiple samples.
+`pycoMeth` can be used for further analyses starting from the output files generated by [`Nanopolish call-methylation`](https://github.com/jts/nanopolish). The package contains a suite of tools to **find CpG islands** calculate the **methylation probability at CpG dinucleotide or CpG island resolution** across the entire genome and to perform a **simple differential methylation analysis** across multiple samples.
 
 The package contains the following modules:
 
@@ -13,7 +21,9 @@ The package contains the following modules:
 * [Meth_Comp](Meth_Comp/usage): Compare Methylation level between several samples from either `pycoMeth CpG_Aggregate` or `pycoMeth Interval_Aggregate`.
 * [CGI_Finder](CGI_Finder/usage): Find CpG islands in a fasta file by using a sliding window and merging overlapping windows satisfying the CpG island definition.
 
-All the tools in `pycoMeth` can generate BED files compatible with any genomic viewer and more extensive tabulated reports allowing users to dig even deeper into the data.
+`pycoMeth` generates extensive tabulated reports and BED files which can be loaded in a genome browser. However, this is not a visualisation tool *per se*. An excellent complementary tool to visualise and explore methylation status for specific loci is [`Methplotlib`](https://github.com/wdecoster/methplotlib) developed by [Wouter de coster](https://twitter.com/wouter_decoster).
+
+Please be aware that `pycoMeth` is a research package that is still under development. The API, command line interface, and implementation might change without retro-compatibility.
 
 ---
 
@@ -23,4 +33,4 @@ All the tools in `pycoMeth` can generate BED files compatible with any genomic v
 
 ### pycoMeth example output IGV rendering
 
-![](pictures/pycoMeth_all.png)
+![](pictures/pycoMeth_all.png)

pycoMeth/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
 
 # Define self package variable
-__version__ = "0.2.9"
+__version__ = "0.3.0"
 __description__ = 'Python package for nanopore DNA methylation analysis downstream to Nanopolish'

setup.py

@@ -5,7 +5,7 @@
 
 # Define package info
 name = "pycoMeth"
-version = "0.2.9"
+version = "0.3.0"
 description = 'Python package for nanopore DNA methylation analysis downstream to Nanopolish'
 with open("README.md", "r") as fh:
     long_description = fh.read()