STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs maths.genealogy
A side-by-side editorial comparison of GeneNMF and maths.genealogy — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs maths.genealogy: at a glance
What is GeneNMF?
GeneNMF rebuilt how it derives meta-programs, changing every result it had produced.
GeneNMF applies non-negative matrix factorization to single-cell expression data to find gene programs, then consolidates programs recurring across samples into meta-programs. Version 0.6.0 replaced the consolidation method: instead of reducing each program to a gene set and taking a consensus, it retains full gene weight vectors and compares them by cosine similarity. Later releases have built reporting and control around that core — a metaprogram composition matrix showing which samples contributed, custom signature databases for enrichment testing, and the ability to drop meta-programs from results.
What is maths.genealogy?
A young Mathematics Genealogy client spending its first four releases satisfying CRAN.
maths.genealogy queries the Mathematics Genealogy Project over a WebSocket connection and renders academic advisor-student trees, with plot_grviz() as the visualisation entry point. The package reached CRAN in early 2025 and its functional surface has barely moved since — max_zoom() for deep trees at 0.1.1 is the only user-facing addition in the visible history.
GeneNMF vs maths.genealogy: editorial side-by-side
GeneNMF
0.0ANALYTICS
GeneNMF rebuilt how it derives meta-programs, changing every result it had produced.
◆ Current state
GeneNMF applies non-negative matrix factorization to single-cell expression data to find gene programs, then consolidates programs recurring across samples into meta-programs. Version 0.6.0 replaced the consolidation method: instead of reducing each program to a gene set and taking a consensus, it retains full gene weight vectors and compares them by cosine similarity. Later releases have built reporting and control around that core — a metaprogram composition matrix showing which samples contributed, custom signature databases for enrichment testing, and the ability to drop meta-programs from results.
◆ Where it's heading
The package is moving from producing meta-programs to letting users interrogate and constrain how they were formed. Composition matrices, the drop function and downsampled similarity heatmaps all serve inspection rather than derivation. The parameters added alongside the 0.6.0 rewrite — specificity weighting, cumulative weight thresholds, confidence defined as the fraction of programs containing a gene — turn what were fixed internal choices into stated, tunable ones.
◆ Prediction
Recent releases have been fixes and compatibility work rather than method changes, so the core approach appears settled. The dependency on an RcppML version not on CRAN is the loose end most likely to force the next release.
maths.genealogy
0.0ANALYTICS
A young Mathematics Genealogy client spending its first four releases satisfying CRAN.
◆ Current state
maths.genealogy queries the Mathematics Genealogy Project over a WebSocket connection and renders academic advisor-student trees, with plot_grviz() as the visualisation entry point. The package reached CRAN in early 2025 and its functional surface has barely moved since — max_zoom() for deep trees at 0.1.1 is the only user-facing addition in the visible history.
◆ Where it's heading
Every release after the first is CRAN policy management. Three consecutive entries deal with the same underlying problem: examples that hit a live network resource and therefore fail unpredictably on check machines. The progression from wrapping them in \donttest{} to catching a stray case to rewriting all examples against published API-package guidance shows the maintainer converging on a pattern rather than adding features. That is the normal cost of shipping a network client to CRAN, and it appears to be settling.
◆ Prediction
With the examples problem resolved, the next release is the first plausible opportunity for feature work — likely on the plotting side, given max_zoom() was the sole non-compliance change so far. The entries do not name anything specific in progress.
Alternatives to GeneNMF and maths.genealogy
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 GeneNMF or maths.genealogy.
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.
See all GeneNMF alternatives → · See all maths.genealogy alternatives →
Recent activity from GeneNMF and maths.genealogy
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agomaths.genealogyExamples rewritten to CRAN API-package guidance
- 1y agomaths.genealogyRemaining network-dependent example wrapped in donttest
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agomaths.genealogyDESCRIPTION quoting and donttest example wrapping
- 1y agomaths.genealogyplot_grviz() gains max_zoom for deep trees
- 1y agoGeneNMFSimilarity heatmap downsampling and meta-program removal
- 2y agoGeneNMFMeta-programs rebuilt on gene weight vectors and cosine similarity ⚡
- 2y agoGeneNMFFirst stable release published to CRAN
Frequently asked questions
What is the difference between GeneNMF and maths.genealogy?
Both compete on the same themes — r-package — within Analytics. GeneNMF and maths.genealogy 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 GeneNMF better than maths.genealogy?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and maths.genealogy 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 GeneNMF?
Top GeneNMF alternatives in Analytics are ranked by recent ship velocity. Browse the "GeneNMF alternatives" section above for the current picks, or visit /alternatives/genenmf for the full list with editorial commentary on each.
What are the best alternatives to maths.genealogy?
Top maths.genealogy alternatives in Analytics are ranked by recent ship velocity. Browse the "maths.genealogy alternatives" section above for the current picks, or visit /alternatives/maths-genealogy for the full list with editorial commentary on each.