STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs slope
A side-by-side editorial comparison of GeneNMF and slope — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs slope: 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 slope?
A year after gutting itself for a C++ rewrite, SLOPE is back to polishing the interface
SLOPE fits sorted L-one penalized regression models. In July 2025 it replaced its entire solver with the external libslope C++ library, removing the ADMM solver, dropping debugging fields, changing alpha scaling and warning users directly that the breakage was extensive. The releases since have rebuilt convenience on top of that core: summary() and refit() methods for cross-validated objects, automatic refitting in cvSLOPE(), and a threading default reduced from half the available cores to one.
GeneNMF vs slope: 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.
slope
0.0ANALYTICS
A year after gutting itself for a C++ rewrite, SLOPE is back to polishing the interface
◆ Current state
SLOPE fits sorted L-one penalized regression models. In July 2025 it replaced its entire solver with the external libslope C++ library, removing the ADMM solver, dropping debugging fields, changing alpha scaling and warning users directly that the breakage was extensive. The releases since have rebuilt convenience on top of that core: summary() and refit() methods for cross-validated objects, automatic refitting in cvSLOPE(), and a threading default reduced from half the available cores to one.
◆ Where it's heading
The arc runs rewrite, then repair, then convenience. The 1.2.0 release is the repair phase — coefficients_scaled was returning unscaled values, which silently affected every coef.SLOPE() call — and 2.0.0 onward is convenience, with refit() now working without re-supplying training data. The tag timestamps are non-monotonic: 1.0.1 is stamped a minute after 1.1.0 despite the lower version, so ordering here reflects when tags were pushed, not what superseded what.
◆ Prediction
With the cross-validation workflow now closing itself out through automatic refitting, further work is more likely to extend the summary and plotting surface than to touch the solver again.
Alternatives to GeneNMF and slope
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 slope.
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 slope alternatives →
Recent activity from GeneNMF and slope
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 2mo agosloperefit() defaults to training data; class-mismatch scoring fixed
- 6mo agoslopeCross-validation now refits automatically and gains summary methods
- 9mo agoslopeSingle-threaded by default, interruptible, and a scaling bug fixed
- 9mo agoslopeM1 Mac test fix
- 9mo agoslopeGlioma gene expression dataset added
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agoslopeSLOPE 1.0.0 ⚡
- 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
Frequently asked questions
What is the difference between GeneNMF and slope?
Both compete on the same themes — r-package — within Analytics. GeneNMF and slope 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 slope?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and slope 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 slope?
Top slope alternatives in Analytics are ranked by recent ship velocity. Browse the "slope alternatives" section above for the current picks, or visit /alternatives/slope for the full list with editorial commentary on each.