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Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
qtl2 vs sdsfun
A side-by-side editorial comparison of qtl2 and sdsfun — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
qtl2 vs sdsfun: at a glance
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.
What is sdsfun?
A spatial-statistics utility package exists to be depended on, and is built accordingly.
sdsfun collects spatial data science utilities — neighbour lists, spatial constrained clustering, discretization, dummy variable generation, geographical detector statistics and projection helpers — with the computationally heavy parts implemented in Rcpp. It was assembled quickly across late 2024, adding a function set roughly every three weeks, and has slowed since to a couple of releases a year. The most recent work is corrective: no longer initializing the RNG state at load, fixing matrix inputs misread as vectors, and clearing an Armadillo deprecation.
qtl2 vs sdsfun: editorial side-by-side
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.
sdsfun
0.0ANALYTICS
A spatial-statistics utility package exists to be depended on, and is built accordingly.
◆ Current state
sdsfun collects spatial data science utilities — neighbour lists, spatial constrained clustering, discretization, dummy variable generation, geographical detector statistics and projection helpers — with the computationally heavy parts implemented in Rcpp. It was assembled quickly across late 2024, adding a function set roughly every three weeks, and has slowed since to a couple of releases a year. The most recent work is corrective: no longer initializing the RNG state at load, fixing matrix inputs misread as vectors, and clearing an Armadillo deprecation.
◆ Where it's heading
This is infrastructure for a family of packages rather than an end-user tool, and the changelog says so directly — functions were added to support gdverse and sesp, and moran_test was migrated in from geocomplexity. That migration pattern is the defining move: capability consolidates here so the downstream packages can share it instead of each carrying its own copy. Growth has slowed as that consolidation completed, leaving correctness and dependency upkeep.
◆ Prediction
Given the package moves when its dependents need something, the next release most likely brings in another shared function or responds to a downstream requirement rather than following its own plan. Armadillo and CRAN check changes remain the reliable source of maintenance work.
Alternatives to qtl2 and sdsfun
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 qtl2 or sdsfun.
ggtrace
A debugger for ggplot2's internals, hardening its grip as the internals it traces keep moving.
kde1d
A univariate density estimator that added zero-inflated data and reopened its C++ API to do it.
svines
Stationary vine copulas for time series, released in lockstep with the rest of Nagler's vine stack.
gghighlight
A single-purpose ggplot2 extension that has spent six years tracking ggplot2 instead of growing.
rtrek
A Star Trek data package that became a Memory Alpha web client and has been patching scrapers ever since.
Recent activity from qtl2 and sdsfun
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 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
- 10mo agosdsfunPackage load stops touching the RNG state
- 1y agoqtl2Finer-grained parallelism for kinship-based scans
- 1y agoqtl2CSV readers renamed to avoid the readr collision
- 1y agosdsfunUnified partial correlation testing and head/tails discretization
- 1y agosdsfunMissing-value handling added to linear trend removal
- 1y agosdsfunCovariate-based detrending and long-to-matrix spatial reshaping
- 1y agosdsfunSpatially constrained hierarchical clustering and SPADE estimation
- 1y agosdsfunFast geodetector q-value estimator added
Frequently asked questions
What is the difference between qtl2 and sdsfun?
Both compete on the same themes — r-package — within Analytics. qtl2 is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is qtl2 better than sdsfun?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. qtl2 is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. For your specific use case, the alternatives sections above list other Analytics products to evaluate alongside.
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.
What are the best alternatives to sdsfun?
Top sdsfun alternatives in Analytics are ranked by recent ship velocity. Browse the "sdsfun alternatives" section above for the current picks, or visit /alternatives/sdsfun for the full list with editorial commentary on each.