benjeffery
Creating scientific software at http://www.bdi.ox.ac.uk/ Principal dev of the tskit ecosystem.
Oxford UniversityOxford, UK
Pinned Repositories
ilcsoft-py
ILCSoft install script
lcfivertex
LCFI Vertex Package
lciotools
Python tools for LCIO
pycraft
Python Server for StartCraft Brood War API ProxyBot
react-plotlyjs
ReactJS / PlotlyJS integration. Draw plotly.js graphs in your react app.
tsinfer-snakemake
A snakemake workflow for using tsinfer
panoptes
Eyes on your (genomic) data
msprime
Simulate genealogical trees and genomic sequence data using population genetic models
tskit
Population-scale genomics
benjeffery's Repositories
benjeffery/tsinfer-snakemake
A snakemake workflow for using tsinfer
benjeffery/bio2zarr
Convert bioinformatics file formats to Zarr
benjeffery/cyvcf2
cython + htslib == fast VCF and BCF processing
benjeffery/gel-upload
benjeffery/kastore
The key-array store for read-only numerical data.
benjeffery/kastore-feedstock
A conda-smithy repository for kastore.
benjeffery/msprime
A reimplementation of Hudson's classical ms simulator for modern data sets.
benjeffery/msprime-feedstock
A conda-smithy repository for msprime.
benjeffery/progen-2023
tskit poster for probgen 2023
benjeffery/pyodide
Pyodide is a Python distribution for the browser and Node.js based on WebAssembly
benjeffery/pyslim
Tools for dealing with tree sequences coming to and from SLiM.
benjeffery/scikit-allel
A Python package for exploring and analysing genetic variation data
benjeffery/sgkit
Statistical genetics toolkit
benjeffery/sgkit-publication
Sgkit publication repository
benjeffery/tsconvert
Utilities for converting tree sequences to and from other formats
benjeffery/tsdate
Infer the age of ancestral nodes in a tree sequence
benjeffery/tsinfer
Infer a tree sequence from genetic variation data
benjeffery/tsinfer-feedstock
A conda-smithy repository for tsinfer.
benjeffery/tsinfer-qc
Utilities for evaluating tsinfer inferences
benjeffery/tskit
The tree sequence toolkit
benjeffery/tskit-book-theme
A book theme for documentation of tskit projects
benjeffery/tskit-feedstock
A conda-smithy repository for tskit.
benjeffery/tskit-paper
benjeffery/tskit-site
tskit website
benjeffery/tstrait
benjeffery/tszip
Gzip-like compression for tskit tree sequences
benjeffery/tutorials
A set of tutorials for msprime and tskit.
benjeffery/vcf-zarr-publication
Manuscript and associated scripts for vcf-zarr publication
benjeffery/witneypolling
benjeffery/zarr-python
An implementation of chunked, compressed, N-dimensional arrays for Python.