BenjaminSchwessinger's repositories
Structured-birth-death-model
Population structure using the multi-type birth-death model
mmtf-genomics
Methods for mapping genomic data onto 3D protein structure.
Skyline-plots
Inference of past population dynamics using Bayesian Coalescent Skyline and Birth-Death Skyline plots.
MCScanX
MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
2019_EMBL-ABR_Snakemake_webinar
Scripts and Snakemake pipeline used in the EMBL-ABR webinar
python-novice-gapminder
Introduction to Python for non-programmers using gapminder data
quickmerge
A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
2019-parallel-python
Parallel python class material for the 2019 summer school in Canberra.
2019-cython-and-numba
Cython and numba class material for the 2019 summer school in Canberra.
2019-data-tidying-and-visualisation
Data vizualisation class materials for the 2019 summer school in Canberra.
2019-debugging
Debugging lesson for ASPP Apac 2019 in Canberra
2019-advanced-python
Advanced python class material for the 2019 summer school in Canberra.
2019-advanced-numpy
Advanced NumPy materials for the 2019 summer school in Canberra.
aspp-visualisation
Exercises and data for the ASPP Visualisation and Tidy Data workshop
code-for-the-world
A tutorial for Advanced Scientific Python Programming on organizing, documenting, and distributing code
2019-testing-code
Testing code materials for the 2019 summer school in Canberra.
RainCloudPlots
Code and tutorials to visualise your data that is both beautiful *and* statistically valid
CladeAge-Tutorial
Fossil-based divergence-time estimation with CladeAge
POREquality
This is an early version of POREquality, an R Markdown document designed to be ran as part of a Nanopore local basecalling pipeline.
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
scholar.py
A parser for Google Scholar, written in Python
Bacter-Tutorial
Taming the BEAST Tutorial for Bacter
species-tree-clocks
Using StarBEAST2 with species tree relaxed clocks, for Taming the BEAST in the South Pacific
NCI_setup_help
Some short explanations on how to set stuff up on NCI for MinION and other long read analysis
Substitution-model-averaging
A tutorial using bModelTest
Troubleshooting
Post-processing and improving performance
FALCON-Phase
FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds