bodkan

slendr

Population genetic simulations in R 🌍

admixr

An R package for reproducible and automated ADMIXTOOLS analyses

demografr

Fast and simple simulation-based population genetic inference in R

archaic-ychr

Repository of code for the paper "The evolutionary history of Neandertal and Denisovan Y chromosomes" by Petr et al.

ku-popgen2022

Lecture notes and materials on simulations for the 2022 popgen course at Copenhagen University

nea-over-time

Source code and Jupyter notebooks for the paper: "The limits of long-term selection against Neandertal introgression"

vcf2eigenstrat

A simple shell script for VCF -> EIGENSTRAT conversion

adventofcode2021

🎄 Advent of Code 2021 in R 🎄

bam-caller

A simple Python CLI program for calling pseudo-haploid genotypes from BAM files

ku-popgen2023

Lecture notes and materials on simulations for the 2023 popgen course at Copenhagen University

mpieva-slendr-2023

Gentle introduction to population genetic simulations at MPI EVA (2023)

probgen2022

Interactive code examples from the ProbGen 2022 slendr poster

slimr

R package for parsing, processing and analysing SLiM output files.

smbe2021

Companion repository for the SMBE 2021 poster "A framework for simulating spatio-temporal population genomic data on a real geographic landscape"

admixr-SI

admixr-workshop

arch-finder

Scan archaic and modern human genomes to get a list of putatively introgressed alleles

bdkn

A set of personal convenience R functions

bodkan

bodkan.github.io

demography

dotfiles

Personal collection of configuration files I'm using across various machines (my Macbook Pro, GNU/Linux remote nodes and containers)

globe-slendr-2023-03-22

Simulation workshop for the Globe Institute, University of Copenhagen

hg19-bvalues

Conversion of McVicker et al. B value coordinates to hg19

introgression-sims

ku-introgression2024

notebooks

A random collection of exploratory Jupyter notebooks.

spatial-selection

st-locator

tskit

Analyse, create and manipulate tree sequences.