STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs rfm
A side-by-side editorial comparison of GeneNMF and rfm — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs rfm: 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 rfm?
A customer segmentation package that went quiet for six years and returned with dependency hygiene
rfm computes recency, frequency and monetary segmentation for customer analytics in R. The feature surface was set early: 0.1.0 shipped a Shiny app and customer-level input, 0.2.0 added default segments and median statistics, 0.2.1 added user-specified score thresholds and returnable plot objects. Then nothing for nearly six years. Version 0.4.0 in April 2026 fixes a missing-column error and a customer id fault, and moves plotly and gganimate from Suggests to Imports.
GeneNMF vs rfm: 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.
rfm
0.0ANALYTICS
A customer segmentation package that went quiet for six years and returned with dependency hygiene
◆ Current state
rfm computes recency, frequency and monetary segmentation for customer analytics in R. The feature surface was set early: 0.1.0 shipped a Shiny app and customer-level input, 0.2.0 added default segments and median statistics, 0.2.1 added user-specified score thresholds and returnable plot objects. Then nothing for nearly six years. Version 0.4.0 in April 2026 fixes a missing-column error and a customer id fault, and moves plotly and gganimate from Suggests to Imports.
◆ Where it's heading
The 0.4.0 release says more about maintenance posture than about product direction — the version jump past 0.3.x with only two bug fixes and a dependency reshuffle suggests a package being brought back to a releasable state rather than resuming development. Promoting plotly and gganimate to Imports makes the visualization stack mandatory, which is a heavier install in exchange for a simpler code path. The core RFM computation itself has not changed in this window.
◆ Prediction
The entries show a package returning from dormancy rather than pursuing a roadmap, so further small fixes are more likely than new segmentation capability.
Alternatives to GeneNMF and rfm
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 rfm.
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.
Recent activity from GeneNMF and rfm
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 3mo agorfmrfm 0.4.0
- 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
- 6y agorfmrfm 0.2.2
- 6y agorfmrfm 0.2.1
- 7y agorfmrfm 0.2.0
- 8y agorfmrfm 0.1.1
- 8y agorfmrfm 0.1.0
Frequently asked questions
What is the difference between GeneNMF and rfm?
Both compete on the same themes — r-package — within Analytics. GeneNMF and rfm 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 rfm?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and rfm 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 rfm?
Top rfm alternatives in Analytics are ranked by recent ship velocity. Browse the "rfm alternatives" section above for the current picks, or visit /alternatives/rfm for the full list with editorial commentary on each.