https://jonotuke.r-universe.devRecent package updates in jonotukeR-universehttps://github.com/jonotuke.pnghttps://jonotuke.r-universe.devWed, 15 Apr 2026 23:58:36 GMTsimon.tuke@adelaide.edu.au (Jono Tuke)The goal of the package is to provide an easy-to-use method for estimating degrees of relatedness (up to the second degree) for extreme low-coverage data. The package also allows users to quantify and visualise the level of confidence in the estimated degrees of relatedness.https://github.com/r-universe/jonotuke/actions/runs/24488077375Wed, 15 Apr 2026 23:58:36 GMTBREADR1.0.4successhttps://jonotuke.r-universe.devhttps://github.com/jonotuke/breadrexample-pipeline.Rmdexample-pipeline.htmlExample BREADR Analysis2025-04-02 00:06:342026-04-15 23:58:36simon.tuke@adelaide.edu.au (Jono Tuke)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).https://github.com/r-universe/jonotuke/actions/runs/23883802324Thu, 02 Apr 2026 02:02:21 GMTRChASM1.0.0.9000successhttps://jonotuke.r-universe.devhttps://github.com/jonotuke/rchasmexample_analysis.Rmdexample_analysis.htmlExample ChASM Analysis Using Example Data2026-01-08 11:25:472026-04-02 02:02:21