GeneNMF vs qtl2

qtl2 is the R toolkit for QTL mapping in experimental crosses, covering genotype probability calculation, genome scans with and without polygenic effects, permutation testing, SNP association, and the plotting that goes with them. The last year of work has pushed hard in two directions: tooling for high-throughput expression and protein QTL studies, and a generalisation of the scan engine itself so the log-likelihood being maximised can be supplied by the user. Note that the release history reached this feed out of order, so feed position is not a reliable guide to which release came first.

The eQTL and pQTL direction is the clearest thread — cis-trans plots, hotspot counting over a sliding window, multi-trait scan heat maps, and genome-wide genotype plots all arrived together, which is the toolkit an experiment with thousands of traits needs rather than one with a handful. Running underneath it is a steady generalisation of the core: a scan function that accepts an arbitrary likelihood, permutations that work with alternative scan functions, full variance-covariance output from single-position fits. Performance and parallelism get attention each cycle, including a more considerate default that leaves one core free. The rest is the ordinary maintenance of a long-lived package — renames to avoid tidyverse collisions, compiler warnings, and correctness fixes on specific cross types.

With scan1gen and permutation support for alternative scan functions in place, the natural next step is more model types built on that hook rather than more special-cased scan functions; the entries do not indicate which models are planned.