nflreadr
The nflverse data loader, whose releases are dictated by the NFL calendar and CRAN's archive policy
Comparison · Analytics
moderndive vs qtl2
A side-by-side editorial comparison of moderndive and qtl2 — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
moderndive vs qtl2: at a glance
What is moderndive?
The ModernDive teaching package learns to render inside the browser that runs its own textbook
moderndive supplies the datasets, regression helpers and ggplot geoms used by the ModernDive introductory statistics textbook. Its release history is mostly dataset accumulation — much of it contributed by students in batches — punctuated by occasional function work. The latest release is different: it fixes View() so it renders inside webR, the in-browser R that powers the book's live exercises, and reworks the regression helpers to survive in-formula transformations.
What is qtl2?
The standard QTL mapping package in R opened its genome scan to user-supplied likelihood models.
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.
moderndive vs qtl2: editorial side-by-side
moderndive
2.5ANALYTICS
The ModernDive teaching package learns to render inside the browser that runs its own textbook
◆ Current state
moderndive supplies the datasets, regression helpers and ggplot geoms used by the ModernDive introductory statistics textbook. Its release history is mostly dataset accumulation — much of it contributed by students in batches — punctuated by occasional function work. The latest release is different: it fixes View() so it renders inside webR, the in-browser R that powers the book's live exercises, and reworks the regression helpers to survive in-formula transformations.
◆ Where it's heading
The package is following the textbook's second edition into the browser. webR has no pandoc, so the DT htmlwidget path the package relied on cannot produce the self-contained HTML the notebook cell needs, and the auto-print path was gated behind interactive() being false — meaning students working through the live exercises saw an explanatory message where a table should have been. Building a static HTML table and pushing it through webR's viewer hook is a small change with a direct effect on whether the book's interactive mode works at all.
◆ Prediction
With the book's v2 datasets landed and the browser rendering path fixed, the remaining friction is most likely in other functions that assume a desktop R session.
qtl2
2.5ANALYTICS
The standard QTL mapping package in R opened its genome scan to user-supplied likelihood models.
◆ Current state
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.
◆ Where it's heading
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.
◆ Prediction
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.
Alternatives to moderndive and qtl2
Other Analytics products tracked by Sparkpulse, ranked by recent ship velocity. Each card links to a full editorial trajectory and lets you pivot into a head-to-head comparison with either moderndive or qtl2.
susier
Fine-mapping workhorse susieR spends its releases hunting null-effect trimming bugs
UCell
A rank-based gene signature scorer that has grown by adapting to whatever object format single-cell R uses next
detectseparation
A diagnostic package that generalized past its own name, then learned to say which kind of separation it found
brglm2
A bias-reduction package reaches 1.0 by adding an estimator built for high-dimensional logistic regression
bayestools
The JAGS toolkit under RoBMA, shipping the standardization machinery its downstream rewrite needed
See all moderndive alternatives → · See all qtl2 alternatives →
Recent activity from moderndive and qtl2
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 12d agomoderndiveView() renders in webR; regression helpers survive formula transforms
- 27d agoqtl2chr_lengths() extended to cross2 objects
- 1mo agoqtl2A genome scan that takes your own likelihood function ⚡
- 2mo agoqtl2Hotspot counting and cis-trans plots for eQTL studies
- 3mo agoqtl2Confidence interval plotting, plus a documentation correction
- 1y agoqtl2Finer-grained parallelism for kinship-based scans
- 1y agoqtl2CSV readers renamed to avoid the readr collision
- 1y agomoderndiveDatasets and tidy_summary() for the second edition
- 2y agomoderndiveAlmond and flight datasets for the inference chapters
- 4y agomoderndiveTen student-curated teaching datasets
- 4y agomoderndiveAlaska flights subset added
- 5y agomoderndiveCleaner regression tables and an explicit conf.level argument
Frequently asked questions
What is the difference between moderndive and qtl2?
Both compete on the same themes — r-package — within Analytics. moderndive and qtl2 are shipping at a similar cadence (velocity 2.5 vs 2.5, both within Sparkpulse's "active" band). See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is moderndive better than qtl2?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. moderndive and qtl2 are shipping at a similar cadence (velocity 2.5 vs 2.5, both within Sparkpulse's "active" band). For your specific use case, the alternatives sections above list other Analytics products to evaluate alongside.
What are the best alternatives to moderndive?
Top moderndive alternatives in Analytics are ranked by recent ship velocity. Browse the "moderndive alternatives" section above for the current picks, or visit /alternatives/moderndive for the full list with editorial commentary on each.
What are the best alternatives to qtl2?
Top qtl2 alternatives in Analytics are ranked by recent ship velocity. Browse the "qtl2 alternatives" section above for the current picks, or visit /alternatives/qtl2 for the full list with editorial commentary on each.