widdowquinn/notebooks widdowquinn/notebooks

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  • Language
    Jupyter Notebook
  • License
    MIT License
  • Created almost 10 years ago
  • Updated about 8 years ago
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Repository Details

iPython notebooks, and supporting files

More Repositories

1

pyani

Application and Python module for average nucleotide identity analyses of microbes.
Python
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2

find_differential_primers

Code for design of diagnostic PCR primers, and metabarcoding markers.
Python
57
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3

ten_great_papers

Ten great papers for wet lab biologists starting out in computational biology
50
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4

Teaching

Code and files used in teaching and training courses.
TeX
30
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5

scripts

Miscellaneous scripts
Python
22
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6

Teaching-Stan-Hierarchical-Modelling

Jupyter notebooks for teaching hierarchical Bayesian modelling with Stan
HTML
21
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7

2018-03-06-ibioic

Teaching materials for 6-7th March 2018 delivery of introductory bioinformatics training course for IBioIC.
HTML
20
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8

Teaching-Data-Visualisation

Presentation and exercises for the Software Sustainability Institute Research Data Visualisation Workshop (RDVW)
HTML
15
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9

Teaching-IBioIC-Intro-to-Bioinformatics

Course materials for the IBioIC Introduction to Bioinformatics training course
HTML
10
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10

pilercrpy

Python package for interacting with PILER-CR CRISPR repeat finding output.
HTML
9
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11

github-best-practice

Links to GitHub best practice articles/blogs etc.
8
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12

KGML

Python code to parse, manipulate, download, and visualise KGML (KEGG markup language) biological pathway data.
Python
8
star
13

Notebooks-Bioinformatics

Jupyter/iPython notebooks related to bioinformatics.
Jupyter Notebook
8
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14

Teaching-EMBL-Plant-Path-Genomics

Presentation and example material for the EMBL Plant and Pathogen Genomics workshop, 8-11 July 2014
Jupyter Notebook
8
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15

sync_rifftrax

Notes on synchronising RiffTrax Just the Jokes with a movie.
Shell
7
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16

Teaching-Comp-Genomics-Vis

Comparative Genomics and Visualisation teaching module
Jupyter Notebook
7
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17

Teaching-Intro-to-Bioinf

Introduction to Bioinformatics training course slides
TeX
5
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18

ncfp

Program and package that retrieves nucleotide coding sequences from NCBI that correspond to a set of input protein sequences.
Python
3
star
19

Teaching-SWC-Lessons

Lesson materials I have used when teaching Software Carpentry
HTML
2
star
20

Presentation-DataVis-Barplots

A presentation on data visualisation, focusing on deficiencies of barplots.
2
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21

SI_Hugouvieux-Cotte-Pattat_2021

Supplementary information for pyani analyses reported in Hugouvieux-Cotte-Pattat et al. (2021) IJSEM, describing the novel genus Paradisiaca
Python
2
star
22

ggplot2_examples

Working through Hadley Wickham's ggplot2 book
1
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23

ColorSpiral

Module to select colours automatically from a spiral in HSV colour space
Python
1
star
24

THAPBI-pycits

Repository for ITS diagnostics development as part of Phytothreats project
HTML
1
star
25

CLIMB

Notes on CLIMB servers
1
star
26

jupyter_demos

Sample notebooks for demonstrating Jupyter
Jupyter Notebook
1
star
27

23andMe

Scripts/functions for working with 23andMe data
Python
1
star
28

pyrbbh

Module to find reciprocal matches/clusters of protein sequences
Python
1
star
29

pyADHoRe

Python code for handling i-ADHoRe output.
Python
1
star
30

mylabbook

Helper scripts for electronic lab book
Python
1
star
31

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.
HTML
1
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