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 parser.
• qtl.coloc: Python implementation of core functions from the R COLOC package.
• 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 .