STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
fastglm vs GeneNMF
A side-by-side editorial comparison of fastglm and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
fastglm vs GeneNMF: at a glance
What is fastglm?
A fast GLM solver stops being one function and becomes a count-model family
fastglm ran C++ IRLS for standard generalized linear models for six years with almost no releases. In May 2026 it added three top-level model types — negative binomial with jointly estimated dispersion, hurdle, and zero-inflated — each with the entire fitting driver in C++ rather than an R loop around a C++ kernel. The following release generalised Firth bias reduction to every standard family across dense, sparse and streaming backends.
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.
fastglm vs GeneNMF: editorial side-by-side
fastglm
0.0ANALYTICS
A fast GLM solver stops being one function and becomes a count-model family
◆ Current state
fastglm ran C++ IRLS for standard generalized linear models for six years with almost no releases. In May 2026 it added three top-level model types — negative binomial with jointly estimated dispersion, hurdle, and zero-inflated — each with the entire fitting driver in C++ rather than an R loop around a C++ kernel. The following release generalised Firth bias reduction to every standard family across dense, sparse and streaming backends.
◆ Where it's heading
The package changed what it is. Through 0.0.3 it was a drop-in replacement for glm() competing on speed; from 0.1.0 it targets the models people leave base R for — MASS::glm.nb, pscl::hurdle, pscl::zeroinfl — and reimplements their full estimation loops natively. The 0.1.1 follow-up is consolidation on that new surface: Firth generalised past binomial logit, SQUAREM acceleration on the zero-inflation EM driver, and a run of clamping guards and initialization fixes on the families most prone to overflow.
◆ Prediction
The numerical-stability work in 0.1.1 clusters on Tweedie and the inverse and sqrt link families, which suggests those paths are the newest and least exercised — expect further correctness fixes there before new model types.
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.
Alternatives to fastglm and GeneNMF
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 fastglm or GeneNMF.
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 fastglm alternatives → · See all GeneNMF alternatives →
Recent activity from fastglm and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 2mo agofastglmFirth generalised to all families, plus SQUAREM and stability fixes
- 3mo agofastglmCRAN release 0.1.0 ⚡
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 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
- 4y agofastglmC++ headers exposed for linking
- 7y agofastglmFirst CRAN release of the C++ IRLS solver
Frequently asked questions
What is the difference between fastglm and GeneNMF?
Both compete on the same themes — r-package — within Analytics. fastglm and GeneNMF 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 fastglm better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. fastglm and GeneNMF 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 fastglm?
Top fastglm alternatives in Analytics are ranked by recent ship velocity. Browse the "fastglm alternatives" section above for the current picks, or visit /alternatives/fastglm for the full list with editorial commentary on each.
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.