STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
collinear vs GeneNMF
A side-by-side editorial comparison of collinear and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
collinear vs GeneNMF: at a glance
What is collinear?
collinear has broken its API twice to stop making the user pick thresholds.
collinear removes multicollinearity from predictor sets through pairwise correlation and VIF filtering, with a preference order deciding which variable survives each conflict. Two major versions in thirteen months each rewrote the interface: 2.0.0 extended every function to any combination of categorical and numeric responses and predictors, and 3.0.0 moved to multiple responses, restructured the output into classed objects, and made both filtering thresholds adaptive by default. Version 3.0.1 is the first release since that is purely repair.
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.
collinear vs GeneNMF: editorial side-by-side
collinear
0.0ANALYTICS
collinear has broken its API twice to stop making the user pick thresholds.
◆ Current state
collinear removes multicollinearity from predictor sets through pairwise correlation and VIF filtering, with a preference order deciding which variable survives each conflict. Two major versions in thirteen months each rewrote the interface: 2.0.0 extended every function to any combination of categorical and numeric responses and predictors, and 3.0.0 moved to multiple responses, restructured the output into classed objects, and made both filtering thresholds adaptive by default. Version 3.0.1 is the first release since that is purely repair.
◆ Where it's heading
The through-line is removing decisions the user was never well placed to make. Preference-order functions were renamed twice — first onto a metric-and-model scheme in 2.0.0, then onto a response-type scheme in 3.0.0 — and f_auto() picks one when none is given; target encoding went from automatic to opt-in; max_cor and max_vif now default to NULL and trigger a data-driven threshold derived from the 75th percentile of pairwise correlations through a sigmoid and a fitted correlation-to-VIF mapping. Each change is defensible and each one broke callers, which is the cost of this approach.
◆ Prediction
3.0.1 moved the example datasets out into a separate spatialData package and fixed four crashes rather than adding anything, so the next release is most likely more consolidation on the 3.0 surface than a fourth interface.
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 collinear 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 collinear 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 collinear alternatives → · See all GeneNMF alternatives →
Recent activity from collinear and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 3mo agocollinearNamespace, NA and sf fixes; example data moves to spatialData
- 8mo agocollinearAdaptive thresholds, multi-response support and a new output class ⚡
- 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
- 1y agocollinearCategorical responses, f_auto() defaults and future-based parallelism ⚡
- 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 collinear and GeneNMF?
They serve adjacent needs but don't currently overlap on shipped themes. collinear 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 collinear better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. collinear 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 collinear?
Top collinear alternatives in Analytics are ranked by recent ship velocity. Browse the "collinear alternatives" section above for the current picks, or visit /alternatives/collinear 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.