Metadata-Version: 2.1
Name: qtl
Version: 0.1.10
Summary: Utilities for analyzing and visualizing QTL data
Author-email: Francois Aguet <francois@broadinstitute.org>
Maintainer-email: Francois Aguet <francois@broadinstitute.org>
License: BSD 3-Clause License
        
        Copyright (c) 2019, The Broad Institute, Inc. and The General Hospital Corporation.
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Project-URL: Repository, https://github.com/broadinstitute/pyqtl.git
Keywords: Quantitative trait loci
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python :: 3
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: bx-python
Requires-Dist: pyBigWig
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: scipy
Requires-Dist: seaborn

## pyQTL

pyQTL is a python module for analyzing and visualizing quantitative trait loci (QTL) data.

The following functionalities are provided:
* `qtl.annotation`: class for working with gene annotations; includes a [GTF](https://www.gencodegenes.org/pages/data_format.html) parser.
* `qtl.coloc`: Python implementation of core functions from the [R COLOC package](https://github.com/chr1swallace/coloc).
* `qtl.io`: functions for reading/writing BED and GCT files.
* `qtl.locusplot`: functions for generating LocusZoom-style regional association plots.
* `qtl.pileup`: functions for visualizing QTL effects in read pileups from, e.g., RNA-seq data.
* `qtl.plot`: plotting functions for QTLs.

### Install
You can install pyQTL using pip:
```
pip3 install qtl
```
or directly from this repository:
```
$ git clone git@github.com:broadinstitute/pyqtl.git
$ cd pyqtl
# set up virtual environment and install
$ virtualenv venv
$ source venv/bin/activate
(venv)$ pip install -e .
```
