widdowquinn/notebooks

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Created almost 10 years ago
Updated almost 8 years ago

widdowquinn/notebooks

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iPython notebooks, and supporting files

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 biology

Teaching

Code and files used in teaching and training courses.

scripts

Miscellaneous scripts

Teaching-Stan-Hierarchical-Modelling

Jupyter notebooks for teaching hierarchical Bayesian modelling with Stan

2018-03-06-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 course

pilercrpy

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.

Jupyter Notebook

Teaching-EMBL-Plant-Path-Genomics

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

Jupyter Notebook

sync_rifftrax

Notes on synchronising RiffTrax Just the Jokes with a movie.

Teaching-Comp-Genomics-Vis

Comparative Genomics and Visualisation teaching module

Jupyter Notebook

Teaching-Intro-to-Bioinf

Introduction to Bioinformatics training course slides

ncfp

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 Carpentry

Presentation-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 Paradisiaca

ggplot2_examples

Working through Hadley Wickham's ggplot2 book

ColorSpiral

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

THAPBI-pycits

Repository for ITS diagnostics development as part of Phytothreats project

CLIMB

Notes on CLIMB servers

jupyter_demos

Sample notebooks for demonstrating Jupyter

Jupyter Notebook

23andMe

Scripts/functions for working with 23andMe data

pyrbbh

Module to find reciprocal matches/clusters of protein sequences

pyADHoRe

Python code for handling i-ADHoRe output.

mylabbook

Helper scripts for electronic lab book

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.