A realistic-ish aDNA simulator

OLD repository for ASAP - NOW reborn into PANE (lm-ut/PANE)

An R Interface to OxCal

The geodata collection of the Ancient World Mapping Center in GeoJSON format.

This repository houses the RMD and HTML files for a class project conducted in Fall 2019 for ANTH 664: Dental Anthropology.

Collection of georeferenced boundaries of world countries and cultural regions for use in mapping historical data on global or continental scale

This book summarises prepared mini-courses for various computational tools and methods in the field of human archaeogenetic data analysis, with a particular emphasis on population genetics.

AncestralPaths is a local ancestry painting technique based on genealogies produced by RELATE. The method aims to assign 'path' ancestries to segments of chromosomes the decribe the path back throu…

A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

Command line scientific data management tool

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

A geom for ggplot to create bump plots

NGSNGS: Next generation simulator for next generation sequencing data

Visualizations of distributions and uncertainty

Lightweight python library for predicting the difficulty of alignments in phylogenetics

Add zoomed inset panels to your ggplot maps

General tools for genomic analyses.

Create a magnified inset of part of a ggplot object

🧹🦷 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

A repository of data and training materials that accompanies the TRAC Webinar: 'Data reuse, digital literacy and the Roman Rural Settlement Project'

Fast and simple simulation-based population genetic inference in R

In this study, it is aimed to make analyzes using ancient metagenome simulations.

generating artificial admixed individuals from given populations by using EIGENSTRAT dataset

This repo contains scripts I use for my work (genetic anthropology, archaeogenetics or what ever you wanna call it). You may modify them to be more compatible with your works. I will try to update …

A 1h intro to aDNA genotype data, stream processing, PCAs and our mobest algorithm

Making imputation easy

Estimates degrees of relatedness (up to the second degree) for extrememly low-coverage data