Stars
Codes to reproduce "Modelling complex traits with ancestral recombination graphs"
A collection of non-portable Fortran usage, standard-conformant or otherwise
Estimation of Recombination Rate and Maternal LD in Half-Sibs
STITCH - Sequencing To Imputation Through Constructing Haplotypes
QUILT: Low coverage whole genome sequence imputation with large reference panels
The fastest VCF/BCF parser in R https://doi.org/10.1093/bioinformatics/btae049
tree-sequence-based likelihood computations under SMC
A Python package for probabilistic state space modeling with JAX
PAGER is an efficient genotype encoding strategy designed to improve the detection of non-additive genetic variation in complex trait association studies. PAGER dynamically encodes genetic variants…
This software is made to take in graph node based family pedigree and simulate genetic information onto that pedigree via SLiM.
Library to allow calling fortran code from python
F90 to Python interface generator with derived type support
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
ArXiv Digest and Personalized Recommendations using Large Language Models
R package that constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model').
Visualize and annotate genomic coverage with ggplot2
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
Software for Testing Accuracy, Reliability and Scalability of Hierarchical computations.