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cff-version: 1.2.0
message: 'To cite package "RChASM" in publications use:'
type: software
license: MIT
title: 'RChASM: Detection of Chromosomal Aneuploidies in Ancient DNA Studies'
version: 1.0.1
doi: 10.32614/CRAN.package.RChASM
abstract: 'An R implementation of ChASM (Chromosomal Aneuploidy Screening Methodology):
  a statistically rigorous Bayesian approach for screening data sets for autosomal
  and sex chromosomal aneuploidies. This package takes as input the number of (deduplicated)
  reads mapping to chromosomes 1-22 and the X and Y chromosomes, and models these
  using a Dirichlet-multinomial distribution. From this, This package returns posterior
  probabilities of sex chromosomal karyotypes (XX, XY, XXY, XYY, XXX and X) and full
  autosomal aneuploidies (trisomy 13, trisomy 18 and trisomy 21). This package also
  returns two diagnostic statistics: (i) a posterior probability addressing whether
  contamination between XX and XY may explain the observed sex chromosomal aneuploidy,
  and (ii) a chi-squared statistic measuring whether the observed read counts are
  too divergent from the underlying distribution (and may represent abnormal sequencing/quality
  issues).'
authors:
- family-names: Rohrlach
  given-names: Adam B.
  email: adam.rohrlach@adelaide.edu.au
  orcid: https://orcid.org/0000-0002-4204-5018
- family-names: Tuke
  given-names: Jono
  email: simon.tuke@adelaide.edu.au
  orcid: https://orcid.org/0000-0002-1688-8951
- family-names: Haak
  given-names: Wolfgang
  email: wolfgang_haak@eva.mpg.de
  orcid: https://orcid.org/0000-0003-2475-2007
repository: https://jonotuke.r-universe.dev
repository-code: https://github.com/jonotuke/RChASM
commit: 6cf17e35826caaddf2ef62b6f0f16d9cc5966616
url: https://jonotuke.github.io/RChASM/
date-released: '2026-04-30'
contact:
- family-names: Tuke
  given-names: Jono
  email: simon.tuke@adelaide.edu.au
  orcid: https://orcid.org/0000-0002-1688-8951