STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs reda
A side-by-side editorial comparison of GeneNMF and reda — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs reda: 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 reda?
A mature recurrent-event toolkit in careful maintenance, shedding weight rather than adding surface.
reda provides nonparametric mean cumulative function estimation, gamma-frailty rate regression, and event-data simulation for recurrent-event survival analysis. The core API settled at 0.5.0 when Recur() replaced Survr() and the MCF internals moved to C++. Everything since has been consolidation: small argument additions, method completions, and CRAN hygiene.
GeneNMF vs reda: 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.
reda
0.0ANALYTICS
A mature recurrent-event toolkit in careful maintenance, shedding weight rather than adding surface.
◆ Current state
reda provides nonparametric mean cumulative function estimation, gamma-frailty rate regression, and event-data simulation for recurrent-event survival analysis. The core API settled at 0.5.0 when Recur() replaced Survr() and the MCF internals moved to C++. Everything since has been consolidation: small argument additions, method completions, and CRAN hygiene.
◆ Where it's heading
The last three releases contain no new modelling capability at all — a dependency reshuffle, a test-example correction, and a print-order fix. The package is being kept installable and correct rather than extended. Its tightest coupling is to splines2, a sibling package from the same maintainer, which supplies the derivative machinery reda depends on.
◆ Prediction
Expect continued small-cadence CRAN-compliance releases tracking ggplot2 and splines2 changes. The entries show no in-progress feature work, so a substantive release would have to arrive without warning from this feed.
Alternatives to GeneNMF and reda
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 reda.
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 reda alternatives →
Recent activity from GeneNMF and reda
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 11mo agoredaggplot2 and grDevices demoted to Suggests
- 1y agoredaTest example and documentation typo fixes
- 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 agoredasimEvent() gains a user-supplied rate bound
- 5y agoredasummary() method completes the Recur object
- 5y agoredaDerivatives sourced from splines2's deriv method
- 6y agoredaMCF estimates can now skip variance computation
Frequently asked questions
What is the difference between GeneNMF and reda?
Both compete on the same themes — r-package — within Analytics. GeneNMF and reda 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 reda?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and reda 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 reda?
Top reda alternatives in Analytics are ranked by recent ship velocity. Browse the "reda alternatives" section above for the current picks, or visit /alternatives/reda for the full list with editorial commentary on each.