widdowquinn/Teaching widdowquinn/Teaching

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Repository Details

Code and files used in teaching and training courses.

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Ten great papers for wet lab biologists starting out in computational biology
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scripts

Miscellaneous scripts
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Teaching-Stan-Hierarchical-Modelling

Jupyter notebooks for teaching hierarchical Bayesian modelling with Stan
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Teaching materials for 6-7th March 2018 delivery of introductory bioinformatics training course for IBioIC.
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Presentation and exercises for the Software Sustainability Institute Research Data Visualisation Workshop (RDVW)
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Course materials for the IBioIC Introduction to Bioinformatics training course
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pilercrpy

Python package for interacting with PILER-CR CRISPR repeat finding output.
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github-best-practice

Links to GitHub best practice articles/blogs etc.
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KGML

Python code to parse, manipulate, download, and visualise KGML (KEGG markup language) biological pathway data.
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Notebooks-Bioinformatics

Jupyter/iPython notebooks related to bioinformatics.
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Teaching-EMBL-Plant-Path-Genomics

Presentation and example material for the EMBL Plant and Pathogen Genomics workshop, 8-11 July 2014
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sync_rifftrax

Notes on synchronising RiffTrax Just the Jokes with a movie.
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Teaching-Comp-Genomics-Vis

Comparative Genomics and Visualisation teaching module
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Teaching-Intro-to-Bioinf

Introduction to Bioinformatics training course slides
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ncfp

Program and package that retrieves nucleotide coding sequences from NCBI that correspond to a set of input protein sequences.
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Teaching-SWC-Lessons

Lesson materials I have used when teaching Software Carpentry
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Presentation-DataVis-Barplots

A presentation on data visualisation, focusing on deficiencies of barplots.
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SI_Hugouvieux-Cotte-Pattat_2021

Supplementary information for pyani analyses reported in Hugouvieux-Cotte-Pattat et al. (2021) IJSEM, describing the novel genus Paradisiaca
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ggplot2_examples

Working through Hadley Wickham's ggplot2 book
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ColorSpiral

Module to select colours automatically from a spiral in HSV colour space
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THAPBI-pycits

Repository for ITS diagnostics development as part of Phytothreats project
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CLIMB

Notes on CLIMB servers
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jupyter_demos

Sample notebooks for demonstrating Jupyter
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23andMe

Scripts/functions for working with 23andMe data
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pyrbbh

Module to find reciprocal matches/clusters of protein sequences
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notebooks

iPython notebooks, and supporting files
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pyADHoRe

Python code for handling i-ADHoRe output.
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mylabbook

Helper scripts for electronic lab book
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2021-01-13_sipbs_workshop

This repository provides a website and MyBinder-based interactive workshop for the 2021 SIPBS Research Day, on using Python to query UniProt.
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