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