A collection of jupyter notebooks and scripts for analyzing and simulation genomic data, focusing on the MXB and MXL genomes.
We'll be using a few standard packages for scientific computing, plotting, and
simulation, as well as a few packages that are in development or that we'll be
using new upcoming features from. Mostly, I'll assume we are using conda and
will install most packages that way, though a few we'll clone directly and
build locally from the dev branch or pip install some alpha version.
Note that we're pulling in the msprime alpha release for version 1.0, which
will be released
conda create -n mxb_tutorial python=3.8 -y
pip install -r requirements.txt
moments is available via conda, but we'll be using some new API, inference,
and plotting features that are in development and haven't been pulled into
a tagged release quite yet. This is why we install from the devel branch.
Risky! But I'm the main developer of moments and will make sure everything
stays working.
Similarly, demesdraw is a package for plotting nice representations of
demographic models using the demes specification, developed primarily
by {user}(grahamgower). That will also get a proper release soon, but we'll also
pull from git for that package as well.
Under the notebooks directory, there are (or will be) a couple of
jupyter-notebooks with examples or tutorials.
Under the models directory, there are a few example, and in the future
inferred, demographic models in demes format.