Pinned Repositories
analysis
Analysis of inference methods on standard population models
discsim
Efficient coalescent simulations in a spatial continuum
ercs
Coalescent simulations in continuous space
msprime-model-errors
A short manuscript describing some modelling errors made with msprime
msprime-paper
Comparisons of simulators for the msprime paper
phylokit
Phylogenetics toolkit for the PyData Ecosystem
python-c-api-demo
A demo of the Python C API for CodeMonkeys
sc2ts
Infer a succinct tree sequence from SARS-COV-2 variation data
sc2ts-paper
jeromekelleher's Repositories
jeromekelleher/phylokit
Phylogenetics toolkit for the PyData Ecosystem
jeromekelleher/sc2ts
Infer a succinct tree sequence from SARS-COV-2 variation data
jeromekelleher/sc2ts-paper
jeromekelleher/cyvcf2
cython + htslib == fast VCF and BCF processing
jeromekelleher/tsinfer
Infer a tree sequence from genetic variation data
jeromekelleher/tskit
The tree sequence toolkit
jeromekelleher/adding-species-manuscript
manuscript materials for the adding species paper
jeromekelleher/bed-reader-feedstock
A conda-smithy repository for bed-reader.
jeromekelleher/bio2zarr
Convert bioinformatics file formats to Zarr
jeromekelleher/demes-paper
Manuscript for the demes package for demographic model specification.
jeromekelleher/divmat
jeromekelleher/ga4gh-client-c
Experimental C client library for the GA4GH API.
jeromekelleher/lshmm
code to run Li and Stephens
jeromekelleher/msprime
Simulate genealogical trees and genomic sequence data using population genetic models
jeromekelleher/msprime-1.0-paper
Publication describing msprime 1.0
jeromekelleher/progen-2023
tskit poster for probgen 2023
jeromekelleher/sgkit
Statistical genetics toolkit
jeromekelleher/sgkit-feedstock
A conda-smithy repository for sgkit.
jeromekelleher/sgkit-publication
Sgkit publication repository
jeromekelleher/slim-feedstock
A conda-smithy repository for slim.
jeromekelleher/smc-bit-paper
Paper on backwards in time SMC description
jeromekelleher/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
jeromekelleher/stdpopsim-feedstock
A conda-smithy repository for stdpopsim.
jeromekelleher/tsinfer-qc
Utilities for evaluating tsinfer inferences
jeromekelleher/tskit-site
tskit website
jeromekelleher/tstrait
jeromekelleher/tstrait-paper
jeromekelleher/vcf-zarr-publication
Manuscript and associated scripts for vcf-zarr publication
jeromekelleher/what-is-an-arg-paper
Manuscript and code for the "What is an ARG?" paper
jeromekelleher/wormtable
Write-once-read-many table for large datasets.