STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs nmar
A side-by-side editorial comparison of GeneNMF and nmar — release velocity, themes, recent moves, and the top alternatives to consider.
GeneNMF vs nmar: 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 nmar?
NMAR landed on CRAN with two nonresponse estimators behind one interface, then started tuning it.
Three releases in seven weeks, starting from nothing. The initial CRAN release implements empirical likelihood (Qin, Leung and Shao 2002) and both parametric and nonparametric exponential tilting (Riddles, Kim and Im 2016) for estimating means under nonignorable nonresponse, all reachable through a single nmar() call with formula syntax and direct support for survey.design objects. Since then the work has been operational: a configurable bootstrap backend and stricter input validation.
GeneNMF vs nmar: 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.
nmar
0.0ANALYTICS
NMAR landed on CRAN with two nonresponse estimators behind one interface, then started tuning it.
◆ Current state
Three releases in seven weeks, starting from nothing. The initial CRAN release implements empirical likelihood (Qin, Leung and Shao 2002) and both parametric and nonparametric exponential tilting (Riddles, Kim and Im 2016) for estimating means under nonignorable nonresponse, all reachable through a single nmar() call with formula syntax and direct support for survey.design objects. Since then the work has been operational: a configurable bootstrap backend and stricter input validation.
◆ Where it's heading
The package is positioning itself as the general interface to nonignorable-nonresponse estimation rather than a reference implementation of one paper — shared architecture across engines, one formula API, and integration with the survey package so weights and stratification come for free. The follow-up releases suggest the next constraint is compute: bootstrap variance estimation is the expensive part, and it now dispatches to future.apply when a parallel plan exists.
◆ Prediction
Expect further engines under the same nmar() interface or wider bootstrap support, since the architecture was explicitly refactored to share structure across estimators.
Alternatives to GeneNMF and nmar
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 nmar.
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 nmar alternatives →
Recent activity from GeneNMF and nmar
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 6mo agonmarBootstrap backend now parallel-aware and configurable
- 7mo agonmarCRAN submission fixes and DOI references
- 8mo agonmarNMAR 0.1.0 ⚡
- 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
Frequently asked questions
What is the difference between GeneNMF and nmar?
They serve adjacent needs but don't currently overlap on shipped themes. GeneNMF and nmar 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 nmar?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and nmar 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 nmar?
Top nmar alternatives in Analytics are ranked by recent ship velocity. Browse the "nmar alternatives" section above for the current picks, or visit /alternatives/nmar for the full list with editorial commentary on each.