Pinned Repositories
2014-06-16-davis
Main repository for the Software Carpentry Workshop at UC Davis on June 16-17 2014
2018_aspp_melbourne_cython
2019-advanced-numpy
Advanced NumPy materials for the 2019 summer school in Canberra.
20191130_ANU
ABC_python
EVM_tools
Some parsers for EVM
NCI_setup_help
Some short explanations on how to set stuff up on NCI for MinION and other long read analysis
Pst_104_E137_A-_genome
This is the shared git repo for the genome analysis of Pst_104E_genome. This was first available as preprint here https://www.biorxiv.org/content/early/2017/09/22/192435 and now published in mBio here https://mbio.asm.org/content/9/1/e02275-17
RainCloudPlots
Code and tutorials to visualise your data that is both beautiful *and* statistically valid
snakemake_recipes
BenjaminSchwessinger's Repositories
BenjaminSchwessinger/Pst_104_E137_A-_genome
This is the shared git repo for the genome analysis of Pst_104E_genome. This was first available as preprint here https://www.biorxiv.org/content/early/2017/09/22/192435 and now published in mBio here https://mbio.asm.org/content/9/1/e02275-17
BenjaminSchwessinger/NCI_setup_help
Some short explanations on how to set stuff up on NCI for MinION and other long read analysis
BenjaminSchwessinger/RainCloudPlots
Code and tutorials to visualise your data that is both beautiful *and* statistically valid
BenjaminSchwessinger/2019-advanced-numpy
Advanced NumPy materials for the 2019 summer school in Canberra.
BenjaminSchwessinger/2019-advanced-python
Advanced python class material for the 2019 summer school in Canberra.
BenjaminSchwessinger/2019-cython-and-numba
Cython and numba class material for the 2019 summer school in Canberra.
BenjaminSchwessinger/2019-data-tidying-and-visualisation
Data vizualisation class materials for the 2019 summer school in Canberra.
BenjaminSchwessinger/2019-debugging
Debugging lesson for ASPP Apac 2019 in Canberra
BenjaminSchwessinger/2019-parallel-python
Parallel python class material for the 2019 summer school in Canberra.
BenjaminSchwessinger/2019-testing-code
Testing code materials for the 2019 summer school in Canberra.
BenjaminSchwessinger/2019_EMBL-ABR_Snakemake_webinar
Scripts and Snakemake pipeline used in the EMBL-ABR webinar
BenjaminSchwessinger/aspp-visualisation
Exercises and data for the ASPP Visualisation and Tidy Data workshop
BenjaminSchwessinger/Bacter-Tutorial
Taming the BEAST Tutorial for Bacter
BenjaminSchwessinger/CladeAge-Tutorial
Fossil-based divergence-time estimation with CladeAge
BenjaminSchwessinger/code-for-the-world
A tutorial for Advanced Scientific Python Programming on organizing, documenting, and distributing code
BenjaminSchwessinger/FALCON-Phase
FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds
BenjaminSchwessinger/Honours_year
BenjaminSchwessinger/MCScanX
MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
BenjaminSchwessinger/mmtf-genomics
Methods for mapping genomic data onto 3D protein structure.
BenjaminSchwessinger/pelita_template
BenjaminSchwessinger/POREquality
This is an early version of POREquality, an R Markdown document designed to be ran as part of a Nanopore local basecalling pipeline.
BenjaminSchwessinger/python-novice-gapminder
Introduction to Python for non-programmers using gapminder data
BenjaminSchwessinger/quickmerge
A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
BenjaminSchwessinger/scholar.py
A parser for Google Scholar, written in Python
BenjaminSchwessinger/Skyline-plots
Inference of past population dynamics using Bayesian Coalescent Skyline and Birth-Death Skyline plots.
BenjaminSchwessinger/species-tree-clocks
Using StarBEAST2 with species tree relaxed clocks, for Taming the BEAST in the South Pacific
BenjaminSchwessinger/Structured-birth-death-model
Population structure using the multi-type birth-death model
BenjaminSchwessinger/Substitution-model-averaging
A tutorial using bModelTest
BenjaminSchwessinger/SynNet-Pipeline
BenjaminSchwessinger/Troubleshooting
Post-processing and improving performance