Prerequisites

psQTL is written in Python and requires a modern version 3. Development occurred using >= 3.11, with its backwards compatibility being as-yet untested.

psQTL makes use of the following Python packages:

• biopython (https://biopython.org/)
• numpy (https://numpy.org/)
• pandas (https://pandas.pydata.org/)
• matplotlib (https://matplotlib.org/)
• ncls (https://github.com/pyranges/ncls)
• pyCirclize (https://moshi4.github.io/pyCirclize/)

It also calls upon the HTSlib (http://www.htslib.org/) programs including:

• samtools
• bcftools
• bgzip

As well as vt (https://genome.sph.umich.edu/wiki/Vt).

If you want to run sPLS-DA analysis on your data, you will also optionally require R (>= 4.5.0) with packages including:

• mixOmics (https://bioconductor.org/packages/release/bioc/html/mixOmics.html)
• BiocParallel (https://www.bioconductor.org/packages/release/bioc/html/BiocParallel.html)
• argparser (https://cran.r-project.org/web/packages/argparser/index.html)
• dplyr (https://cran.r-project.org/web/packages/dplyr/index.html)

psQTL was developed on Linux and within Windows Subsystem for Linux (WSL), although it should work on any system which can run Python, HTSlib, and vt. All external programs should be installed and locateable within your system PATH variable.

See Installing psQTL for details on how to install these software and packages to perform a psQTL analysis.