STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs kde1d
A side-by-side editorial comparison of GeneNMF and kde1d — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs kde1d: 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 kde1d?
A univariate density estimator that added zero-inflated data and reopened its C++ API to do it.
kde1d estimates univariate densities with local polynomial kernel methods, handling bounded, discrete and now zero-inflated variables through a single type argument, with the numerical work in a header-only C++ library usable outside R. Version 1.1.0 added the zero-inflated discrete-continuous mixture case and shipped a new C++ API as an explicit breaking change; 1.1.1 followed in June with auto-generated notes and no description.
GeneNMF vs kde1d: 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.
kde1d
0.0ANALYTICS
A univariate density estimator that added zero-inflated data and reopened its C++ API to do it.
◆ Current state
kde1d estimates univariate densities with local polynomial kernel methods, handling bounded, discrete and now zero-inflated variables through a single type argument, with the numerical work in a header-only C++ library usable outside R. Version 1.1.0 added the zero-inflated discrete-continuous mixture case and shipped a new C++ API as an explicit breaking change; 1.1.1 followed in June with auto-generated notes and no description.
◆ Where it's heading
The package has alternated between performance work and widening the class of data it accepts. The 1.0.0 release was the performance milestone — FFT-based estimation, a better integration algorithm for the p, q and r functions, deterministic jittering replacing randomness, and standalone C++ headers. The 1.1.0 release is the scope milestone, adding a third data type to the two it already handled. Releases come from the same maintainer as svines and cluster on shared dates, so changes in the underlying C++ surface across the vine and density stack tend to ship together.
◆ Prediction
With the C++ API deliberately reworked for standalone use at 1.1.0, further work most plausibly consolidates that interface rather than adding data types. What 1.1.1 actually changed is not readable from its body.
Alternatives to GeneNMF and kde1d
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 kde1d.
ggtrace
A debugger for ggplot2's internals, hardening its grip as the internals it traces keep moving.
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.
eiaapi
A thin EIA energy-data client whose whole story is making bulk queries survive the API's limits.
See all GeneNMF alternatives → · See all kde1d alternatives →
Recent activity from GeneNMF and kde1d
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agokde1dkde1d 1.1.1
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agokde1dZero-inflated mixtures and a new standalone C++ API ⚡
- 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 agokde1dBit-wise Boolean operations removed
- 5y agokde1ddkde1d() invisible output fixed
- 5y agokde1dValgrind false positive silenced
- 6y agokde1dqrng dependency dropped; undefined behaviour fixed
Frequently asked questions
What is the difference between GeneNMF and kde1d?
Both compete on the same themes — r-package — within Analytics. GeneNMF and kde1d 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 kde1d?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and kde1d 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 kde1d?
Top kde1d alternatives in Analytics are ranked by recent ship velocity. Browse the "kde1d alternatives" section above for the current picks, or visit /alternatives/kde1d for the full list with editorial commentary on each.