Software

Source code is available on GitLab or GitHub.

These are projects I had worked on previously. They are not being developed or maintained. If there is an important issue that needs to be fixed, please get in touch with me.

Docker images

I have built Docker images for the following software when required in the research group or as a learning exercise — VIGA, QIIME 1¹, PyFBA, and DADA 2.

These images include programs and their dependencies pre-installed. In some cases, there are wrapper scripts in Bash, that will help users run containers easily, without needing root privileges. You can get these scripts and Dockerfiles from GitLab.

Related blog post
Docker images for Bioinformatics software

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The following projects in this list were developed in research groups as part of a team — RiboPlot, riboSeqR wrapper for Galaxy, IT Query and IT CRISPR. These were all written in Python 2 and are not currently being developed. Python 2 is not supported as of January 2020.

RiboPlot

A Python program to plot and output Ribo-Seq read counts from BAM format alignment files.

This program and the riboSeqR Galaxy wrapper discussed below, were developed under the supervision of Dr. Audrey Michel and Dr. Pasha Baranov at LAPTI, UCC in 2015.

The main program is written in Python 2 and uses the pysam module for working with FASTA and BAM format alignment files. Matplotlib is used for generating plots. HTML output is generated using the Skeleton CSS framework and the Tablesorter JavaScript library is used for sorting the HTML table produced from Ribocount.

You can get RiboPlot from:
PyPI • Anaconda • Galaxy tool shed • GitHub

Documentation is available here.

Galaxy wrapper for riboSeqR

A web interface (XML wrapper) for integrating the riboSeqR R package in RiboGalaxy or Galaxy.

Using the inclued tools, you can prepare input files for riboSeqR from SAM format alignment files, calculate triplet periodicity, perform metagene analysis, plot ribosome profiles, and perform differential translation analysis using baySeq.

You can install riboseqr_wrapper from Galaxy tool shed. Source code is available on GitHub.

BioNumerics 6 GUIs and scripts

These programs were written using Python 2 and PyQt 4 and were developed in collaboration with members in the Microbial Phylogeography group at Environmental Research Institute, UCC during 2007-2012 under the supervision of Prof. Mark Achtman.

Main window of IT Query — IT Query is used for visualizing and managing data from ItemTracker LIMS system

Main window of IT CRISPR — IT CRISPR is used for assembling and tracking the progress of CRISPR sequence experiments

You can get these programs and scripts from GitLab.

GWIPS tools — download genome annotations from UCSC

A collection of Python scripts to download genome annotations and reference sequences from UCSC. You can get them from GitHub.

Other projects

VLinux

A live Linux CD with Bioinformatics software pre-installed².

Themes

Themes for Pelican static site generator and Sphinx documentation generator.

Attila-X

A WIP Pelican theme ⁴ based on Ghost Attila theme.

Susty Pelican

The Wordpress susty ³ theme, ported to Pelican (GitHub).

Solar theme

Sphinx theme using the Solarized colour scheme (GitLab).

QIIME 1 is not supported anymore. Please use QIIME 2. ↩
VLinux is not updated.The ideas from the project are now merged into BioMint. ↩
susty theme for Wordpress. ↩
This is the theme used on this website. ↩

Last updated: Fri 21 July 2023