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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 [email protected]:broadinstitute/pyqtl.git
$ cd pyqtl
# set up virtual environment and install
$ virtualenv venv
$ source venv/bin/activate
(venv)$ pip install -e .