STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs singlercapture
A side-by-side editorial comparison of GeneNMF and singlercapture — release velocity, themes, recent moves, and the top alternatives to consider.
GeneNMF vs singlercapture: 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 singlercapture?
singleRcapture reached 1.0.0 with no release notes at all — the arc has to be read backwards.
A package for single-source capture-recapture population size estimation: zero-truncated Poisson, geometric and negative binomial regression, Chao and Zelterman mixture models, analytic and bootstrap variance estimation, all behind estimatePopsize(). The 0.2.x line professionalised it — an offset argument, parallel bootstrap and dfbeta, faster semiparametric sampling, a singleRStaticCountData subclass explicitly created so a companion package could fit models from countreg and VGAM, then interaction-term and anova fixes. The 1.0.0 release carries nothing but a link to the compare view.
GeneNMF vs singlercapture: 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.
singlercapture
0.0ANALYTICS
singleRcapture reached 1.0.0 with no release notes at all — the arc has to be read backwards.
◆ Current state
A package for single-source capture-recapture population size estimation: zero-truncated Poisson, geometric and negative binomial regression, Chao and Zelterman mixture models, analytic and bootstrap variance estimation, all behind estimatePopsize(). The 0.2.x line professionalised it — an offset argument, parallel bootstrap and dfbeta, faster semiparametric sampling, a singleRStaticCountData subclass explicitly created so a companion package could fit models from countreg and VGAM, then interaction-term and anova fixes. The 1.0.0 release carries nothing but a link to the compare view.
◆ Where it's heading
The direction visible in 0.2.x is outward: refactoring for maintainability, extending to models fitted elsewhere via a subclass, adding a JSS-paper vignette, and pushing coverage towards 90%. That is a package preparing to be cited and extended rather than one still finding its methods. The 1.0.0 tag presumably marks the end of that stabilisation, but the entry itself gives no evidence either way.
◆ Prediction
Not readable from this feed — the 1.0.0 notes are empty, so whether the major version marks an API freeze or a breaking change cannot be determined from the entries shown.
Alternatives to GeneNMF and singlercapture
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 singlercapture.
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 singlercapture alternatives →
Recent activity from GeneNMF and singlercapture
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 6mo agosinglercapturesingleRcapture 1.0.0
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agosinglercaptureanova and other broken methods fixed
- 1y agosinglercaptureInteraction terms fixed; logLik returns gradients and hessians
- 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 agosinglercaptureSubclass opens population estimation to countreg and VGAM fits
- 4y agosinglercaptureFirst usable release: zero-truncated and mixture estimators
Frequently asked questions
What is the difference between GeneNMF and singlercapture?
They serve adjacent needs but don't currently overlap on shipped themes. GeneNMF and singlercapture 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 singlercapture?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and singlercapture 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 singlercapture?
Top singlercapture alternatives in Analytics are ranked by recent ship velocity. Browse the "singlercapture alternatives" section above for the current picks, or visit /alternatives/singlercapture for the full list with editorial commentary on each.