STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
gdverse vs GeneNMF
A side-by-side editorial comparison of gdverse and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
gdverse vs GeneNMF: at a glance
What is gdverse?
gdverse is turning geographical detector methods into inference, not just point estimates.
A geographical detector toolkit for spatial stratified heterogeneity, shipping small numbered releases every few months. Recent work centres on statistical rigour: confidence intervals for the q-statistic (experimental in 1.3-2, made more robust in 1.6), reported significance for interaction detection, and a fix for stratification collision in that same interaction path. The rest is Python-interop maintenance — reticulate compatibility, parallel stability in cpd_disc, and dependency configuration.
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.
gdverse vs GeneNMF: editorial side-by-side
gdverse
0.0ANALYTICS
gdverse is turning geographical detector methods into inference, not just point estimates.
◆ Current state
A geographical detector toolkit for spatial stratified heterogeneity, shipping small numbered releases every few months. Recent work centres on statistical rigour: confidence intervals for the q-statistic (experimental in 1.3-2, made more robust in 1.6), reported significance for interaction detection, and a fix for stratification collision in that same interaction path. The rest is Python-interop maintenance — reticulate compatibility, parallel stability in cpd_disc, and dependency configuration.
◆ Where it's heading
The arc is from computing detector statistics to qualifying them. Confidence intervals, significance reporting and non-centrality parameter estimation are all about telling users how much to trust a q-value, which is the gap between a research script and a package other people cite. The Python-dependency work is the recurring tax on that: several releases exist mainly to keep reticulate-backed models passing checks.
◆ Prediction
Expect the experimental q-statistic confidence intervals to be promoted to a stable, documented interface across the detector family, since the last two releases have both worked on their robustness and reporting.
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.
Alternatives to gdverse and GeneNMF
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 gdverse or GeneNMF.
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 gdverse alternatives → · See all GeneNMF alternatives →
Recent activity from gdverse and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 6mo agogdverseInteraction detection reports significance; stratification collision fixed
- 10mo agogdversePython examples wrapped to stop CRAN check failures
- 10mo agogdversecpd_disc refactored for parallel stability and reticulate compatibility
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agogdverseAdds package citation metadata
- 1y agogdverseExperimental confidence intervals for the q statistic
- 1y agogdversePlot method bug fixes across four detector models
- 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 gdverse and GeneNMF?
They serve adjacent needs but don't currently overlap on shipped themes. gdverse and GeneNMF 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 gdverse better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. gdverse and GeneNMF 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 gdverse?
Top gdverse alternatives in Analytics are ranked by recent ship velocity. Browse the "gdverse alternatives" section above for the current picks, or visit /alternatives/gdverse for the full list with editorial commentary on each.
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.