Metadata-Version: 2.1
Name: scie2g
Version: 1.0.1
Summary: UNKNOWN
Home-page: https://github.com/ArianeMora/sciepi2gene
Author: Ariane Mora
Author-email: ariane.n.mora@gmail.com
License: GPL3
Project-URL: Bug Tracker, https://github.com/ArianeMora/sciepi2gene/issues
Project-URL: Documentation, https://github.com/ArianeMora/sciepi2gene
Project-URL: Source Code, https://github.com/ArianeMora/sciepi2gene
Description: # sci-Epi2Gene
        [![codecov.io](https://codecov.io/github/ArianeMora/sciepi2gene/coverage.svg?branch=master)](https://codecov.io/github/ArianeMora/sciepi2gene?branch=master)
        [![PyPI](https://img.shields.io/pypi/v/scie2g)](https://pypi.org/project/scie2g/)
        [![DOI](https://zenodo.org/badge/316410924.svg)](https://zenodo.org/badge/latestdoi/316410924)
        
        [Link to docs](https://arianemora.github.io/sciepi2gene/)
        
        Sci-epi2gene maps events annotated to a genome location to nearby genes - i.e. peaks from histone modification data
        ChIP-seq experiemnts stored as bed data, or DNA methylation data in csv format (e.g. output from DMRseq, methylKit or methylSig).
        
        The user provides a SORTED gene annotation file with start, end, and direction for each gene (we recommend using
        [sci-biomart](https://github.com/ArianeMora/scibiomart), see examples for detail.
        
        The user then selects how to annotate, i.e. whether it is in the promoter region, or overlaps the gene body. Finally,
        the parameters for overlap on each side are chosen.
        
        It is available under the [GNU General Public License (Version 3) ](https://www.gnu.org/licenses/gpl-3.0.en.html).
        
        This package is a wrapper that allows various epigenetic data types to be annotated to genes. [Examples are in the docs](https://arianemora.github.io/sciepi2gene/)
        
        I also wanted to have different upper flanking and lower flanking distances that took into account the directionality of the strand
        and also an easy output csv file that can be filtered and used in downstream analyses. This is why I keep all features
        that fall within the annotation region of a gene (example below):
        
        The overlapping methods are as follows:
            1) overlaps: this means does ANY part of the peak/feature overlap the gene body + some buffer before the TSS and some buffer on the non-TSS side
            2) promoter: does ANY part of the peak/feature overlap with the TSS of the gene taking into account buffers on either side of the TSS.
        
        .. image:: _static/example_overlaps.png
           :width: 600
        
        As you can see from the above screenshot using IGV, the input peaks are in purple, and the green are the output
        peaks as annotated to genes. The function *convert_to_bed* converts the output csv to bed files for viewing. This example
        shows that a peak/feature can be annotated to multiple genes. Peaks/features outside of the regions of genes (e.g.
        the first peak) are dropped from the output.
        
        We show this example in the notebook (see examples folder), where we use [IGV](https://github.com/igvteam/igv-jupyter#igvjs-jupyter-extension)
        to view the tracks (see image below).
        
        .. image:: _static/igv_jupyter.png
           :width: 600
           
        Lastly, there are sometimes differences between annotations (i.e. the TSS on your annotation in IGV may differ to the
        annotation you input to sciepi2gene), naturally, how your genes/features are annotated depends on the input file so if you see differences check this first!
        
        Please post questions and issues related to sci-epi2gene on the `Issues <https://github.com/ArianeMora/sciepi2gene/issues>`_  section of the GitHub repository.
        
        
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
