simlandr
Potential landscape tooling settling onto standard R generics after two rounds of renaming.
Comparison · Analytics
mmconvert vs STACAS
A side-by-side editorial comparison of mmconvert and STACAS — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
mmconvert vs STACAS: at a glance
What is mmconvert?
A single-purpose mouse map interpolator that solved its problem in 2023 and has coasted since
mmconvert does one thing: interpolate between GRCm39 physical positions and the revised Cox genetic map for mouse MUGA array markers. The substantive work all landed in a burst across 2021-2023 — the initial function, the GRCm39 annotation dataset, cross2_to_grcm39(), the recomputed Cox maps and their smoothed replacement. Everything since is upkeep: a warning-message fix in 0.12, and 0.14 is a test adjustment to silence a CRAN Note with no code change at all.
What is STACAS?
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
STACAS integrates single-cell RNA-seq datasets by finding and weighting anchors between them, with rPCA-distance-based downweighting and an optional semi-supervised mode that uses cell type labels to discard inconsistent anchors. IntegrateData.STACAS() performs the integration natively rather than handing off, and StandardizeGeneSymbols() normalises gene naming across datasets before anchors are computed.
mmconvert vs STACAS: editorial side-by-side
mmconvert
0.0ANALYTICS
A single-purpose mouse map interpolator that solved its problem in 2023 and has coasted since
◆ Current state
mmconvert does one thing: interpolate between GRCm39 physical positions and the revised Cox genetic map for mouse MUGA array markers. The substantive work all landed in a burst across 2021-2023 — the initial function, the GRCm39 annotation dataset, cross2_to_grcm39(), the recomputed Cox maps and their smoothed replacement. Everything since is upkeep: a warning-message fix in 0.12, and 0.14 is a test adjustment to silence a CRAN Note with no code change at all.
◆ Where it's heading
The package has reached the natural end state of a reference-data converter — the reference data stopped moving, so the package stopped moving. Releases now arrive roughly annually and exist to keep CRAN checks green. The 0.14 release shipped the same day as sibling qtl2convert 0.36, confirming these are batch maintenance passes across the maintainer's packages rather than independent development.
◆ Prediction
Without a new mouse genome build or a revised Cox map, the next release is likely another CRAN-check accommodation rather than new functionality.
STACAS
0.0ANALYTICS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
◆ Current state
STACAS integrates single-cell RNA-seq datasets by finding and weighting anchors between them, with rPCA-distance-based downweighting and an optional semi-supervised mode that uses cell type labels to discard inconsistent anchors. IntegrateData.STACAS() performs the integration natively rather than handing off, and StandardizeGeneSymbols() normalises gene naming across datasets before anchors are computed.
◆ Where it's heading
The method work concentrated in version 2.0 and has been stable since; everything after is Seurat compatibility and operational robustness. Versions 2.1.1 through 2.3.0 track Seurat v5 assays, v3-to-v5 conversion, multi-layer objects and SCT normalisation, with the genuinely useful additions — a reference seed dataset, max.seed.datasets for large-scale integration, min.sample.size — arriving as side effects of that work. The package is from the same lab as GeneNMF, and its release rhythm follows the single-cell ecosystem's upstream churn rather than an internal roadmap.
◆ Prediction
Expect the next release to follow further Seurat object-model changes, which have driven the last three. Nothing in the entries indicates new anchor-scoring or correction methodology in progress.
Alternatives to mmconvert and STACAS
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 mmconvert or STACAS.
lavaanExtra
SEM reporting helpers converging on APA output, one CRAN resubmission at a time.
ibis.iSDM
A raster-to-terra migration is the only readable change in a feed of merge notes.
anyflights
A nycflights13 generator whose recent work is all about the data being right.
vinereg
Conditional density and log-likelihood fill out a vine copula regression package.
stringx
A drop-in string API for base R, kept alive by upstream check failures.
See all mmconvert alternatives → · See all STACAS alternatives →
Recent activity from mmconvert and STACAS
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agommconvertTest adjustment to clear a CRAN Note
- 1y agoSTACASMulti-layer objects and Seurat v3-to-v5 conversion handled
- 1y agommconvertFixes a malformed warning message in mmconvert()
- 2y agoSTACASscale.data option for extreme batch effects; gene name conversion table
- 3y agoSTACASReference seeding, gene symbol standardisation, large-scale integration path
- 3y agommconvertOmits X chromosome positions for sex-averaged and male maps
- 3y agommconvertCRAN release adds chromosome lengths and smoothed Cox maps
- 3y agommconvertRecomputed Cox genetic maps and combined-array support
- 4y agoSTACASSemi-supervised integration and rPCA anchor downweighting ⚡
- 4y agommconvertRepoints data sources from master to main branches
- 5y agoSTACASSeurat 4.0.0 compatibility and SCTransform support
Frequently asked questions
What is the difference between mmconvert and STACAS?
Both compete on the same themes — r-package — within Analytics. mmconvert and STACAS are shipping at a similar cadence (velocity 0.0 vs 0.0, 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 mmconvert better than STACAS?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. mmconvert and STACAS are shipping at a similar cadence (velocity 0.0 vs 0.0, 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 mmconvert?
Top mmconvert alternatives in Analytics are ranked by recent ship velocity. Browse the "mmconvert alternatives" section above for the current picks, or visit /alternatives/mmconvert for the full list with editorial commentary on each.
What are the best alternatives to STACAS?
Top STACAS alternatives in Analytics are ranked by recent ship velocity. Browse the "STACAS alternatives" section above for the current picks, or visit /alternatives/stacas for the full list with editorial commentary on each.