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pyani
Application and Python module for average nucleotide identity analyses of microbes.find_differential_primers
Code for design of diagnostic PCR primers, and metabarcoding markers.ten_great_papers
Ten great papers for wet lab biologists starting out in computational biologyTeaching
Code and files used in teaching and training courses.scripts
Miscellaneous scriptsTeaching-Stan-Hierarchical-Modelling
Jupyter notebooks for teaching hierarchical Bayesian modelling with Stan2018-03-06-ibioic
Teaching materials for 6-7th March 2018 delivery of introductory bioinformatics training course for IBioIC.Teaching-Data-Visualisation
Presentation and exercises for the Software Sustainability Institute Research Data Visualisation Workshop (RDVW)Teaching-IBioIC-Intro-to-Bioinformatics
Course materials for the IBioIC Introduction to Bioinformatics training coursepilercrpy
Python package for interacting with PILER-CR CRISPR repeat finding output.github-best-practice
Links to GitHub best practice articles/blogs etc.KGML
Python code to parse, manipulate, download, and visualise KGML (KEGG markup language) biological pathway data.Notebooks-Bioinformatics
Jupyter/iPython notebooks related to bioinformatics.Teaching-EMBL-Plant-Path-Genomics
Presentation and example material for the EMBL Plant and Pathogen Genomics workshop, 8-11 July 2014sync_rifftrax
Notes on synchronising RiffTrax Just the Jokes with a movie.Teaching-Comp-Genomics-Vis
Comparative Genomics and Visualisation teaching moduleTeaching-Intro-to-Bioinf
Introduction to Bioinformatics training course slidesncfp
Program and package that retrieves nucleotide coding sequences from NCBI that correspond to a set of input protein sequences.Teaching-SWC-Lessons
Lesson materials I have used when teaching Software CarpentryPresentation-DataVis-Barplots
A presentation on data visualisation, focusing on deficiencies of barplots.SI_Hugouvieux-Cotte-Pattat_2021
Supplementary information for pyani analyses reported in Hugouvieux-Cotte-Pattat et al. (2021) IJSEM, describing the novel genus Paradisiacaggplot2_examples
Working through Hadley Wickham's ggplot2 bookColorSpiral
Module to select colours automatically from a spiral in HSV colour spaceTHAPBI-pycits
Repository for ITS diagnostics development as part of Phytothreats projectjupyter_demos
Sample notebooks for demonstrating Jupyter23andMe
Scripts/functions for working with 23andMe datapyrbbh
Module to find reciprocal matches/clusters of protein sequencesnotebooks
iPython notebooks, and supporting filespyADHoRe
Python code for handling i-ADHoRe output.mylabbook
Helper scripts for electronic lab book2021-01-13_sipbs_workshop
This repository provides a website and MyBinder-based interactive workshop for the 2021 SIPBS Research Day, on using Python to query UniProt.Love Open Source and this site? Check out how you can help us