STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
fastrg vs GeneNMF
A side-by-side editorial comparison of fastrg and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
fastrg vs GeneNMF: at a glance
What is fastrg?
A fast random-graph sampler that spent 0.3.1 fixing what its parameters actually mean.
fastRG samples from generalized random dot product graphs — stochastic blockmodels, degree-corrected and overlapping variants, directed and undirected — in time proportional to the number of edges rather than nodes squared, which is what makes large sparse networks tractable. Since 0.3.1 the model is constructed and parameterised in one object, with sampling methods taking that object rather than re-specifying edge distribution at sample time.
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.
fastrg vs GeneNMF: editorial side-by-side
fastrg
0.0ANALYTICS
A fast random-graph sampler that spent 0.3.1 fixing what its parameters actually mean.
◆ Current state
fastRG samples from generalized random dot product graphs — stochastic blockmodels, degree-corrected and overlapping variants, directed and undirected — in time proportional to the number of edges rather than nodes squared, which is what makes large sparse networks tractable. Since 0.3.1 the model is constructed and parameterised in one object, with sampling methods taking that object rather than re-specifying edge distribution at sample time.
◆ Where it's heading
The package's development has been about semantic correctness more than speed. The 0.3.1 release moved edge-distribution arguments to the constructors and reinterpreted the mixing matrix S under Bernoulli parameterisation; 0.3.2 then flipped the meaning of X and Y in directed blockmodels so outgoing and incoming factors match the edge convention, and made block sorting conditional rather than unconditional. Both are corrections to what returned values mean, not to how fast they arrive. The 2025 release is CRAN documentation linking only.
◆ Prediction
With parameterisation settled and only a documentation release since 2023, the package reads as feature-complete for its sampling families. Nothing in the entries points to additional model types being queued.
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 fastrg 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 fastrg 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 fastrg alternatives → · See all GeneNMF alternatives →
Recent activity from fastrg and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agofastrgDocumentation cross-linking fixes for CRAN
- 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
- 2y agofastrgDirected blockmodel X and Y factors swapped to match edge direction
- 4y agofastrgfastRG 0.3.1 ⚡
Frequently asked questions
What is the difference between fastrg and GeneNMF?
Both compete on the same themes — r-package — within Analytics. fastrg 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 fastrg better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. fastrg 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 fastrg?
Top fastrg alternatives in Analytics are ranked by recent ship velocity. Browse the "fastrg alternatives" section above for the current picks, or visit /alternatives/fastrg 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.