This repository contains all computational analyses used in my 2020 paper “The evolutionary history of Neandertal and Denisovan Y chromosomes”.
You can find here:
- my complete data processing and data-generation pipeline -
processing of BAM files, genotype calling, simulations
etc. (
Makefile); - scripts used by the
Makefilepipeline (src/) and R functions used for analyses (R/); - R Jupyter notebooks used to generate every result in the paper
(
notebooks/); - cached results in the rds format - useful for re-producing all
tables and figures in the paper without having to first re-process
sequencing data or run SLiM simulations (
data/rds/); for full data access see here.
Note that the repository is structured as an R package, with the
exception that it contains not only the required R package components
(R code in R/, the DESCRIPTION file etc.), but also the data and
analyses themselves. Therefore, after cloning this repository, you can
simply call devtools::load_all(".") from the root of the repository
in an R console and immediately start exploring the data yourself.
All software dependencies used in the project are described in detail in this notebook.
In addition to cached results in data/rds in this repository, all
sequencing data (BAM/VCF/FASTA files), raw simulation outputs, as well
as the sequences of capture probes can be found at:
https://bioinf.eva.mpg.de/archaic-ychr.
In case of trouble, please don’t hesitate to contact me or Janet Kelso.
All software (bash/R/Python scripts) are available under MIT license. The contents of Jupyter notebooks (which include text, figures, tables etc.) and other non-software files in this repository are available under CC BY 4.0 license.