STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs vecvec
A side-by-side editorial comparison of GeneNMF and vecvec — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs vecvec: 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 vecvec?
A vector-of-vectors class swapped its object system mid-flight and came out faster.
vecvec provides an R class that holds multiple vectors as a single logical vector without copying them together, aimed at cases where concatenating would be wasteful. The 1.0.0 rewrite moved the class off vctrs onto S7 while keeping user-facing code working, and added matrix and array behaviour. Recent releases have concentrated on the details that decide whether the abstraction actually saves work: ALTREP vectors surviving intact, subassignment edge cases, and printing that does not materialise what it is describing.
GeneNMF vs vecvec: 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.
vecvec
0.0ANALYTICS
A vector-of-vectors class swapped its object system mid-flight and came out faster.
◆ Current state
vecvec provides an R class that holds multiple vectors as a single logical vector without copying them together, aimed at cases where concatenating would be wasteful. The 1.0.0 rewrite moved the class off vctrs onto S7 while keeping user-facing code working, and added matrix and array behaviour. Recent releases have concentrated on the details that decide whether the abstraction actually saves work: ALTREP vectors surviving intact, subassignment edge cases, and printing that does not materialise what it is describing.
◆ Where it's heading
The arc runs from proving the idea to making it cheap. Early releases established constructors and vctrs dispatch; 1.0.0 rebuilt the internals on S7 with a smaller, faster representation and automatic flattening of adjacent compatible vectors; the two releases since have been about not defeating the point — an ALTREP vector flattened on construction or materialised by a print method gives back exactly the memory the class exists to save. Extensibility is the other visible thread, with custom ptype2 and cast methods now registrable and extension packages expected to subclass class_vecvec. The internal index structure is explicitly reserved for future change, so faster special-case representations look planned rather than incidental.
◆ Prediction
The reserved internal structure and the stated intent to accommodate faster variants point at specialised representations for particular vector types next; the entries do not indicate which cases are queued first.
Alternatives to GeneNMF and vecvec
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 vecvec.
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 vecvec alternatives →
Recent activity from GeneNMF and vecvec
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agovecvecExtension packages can register their own ptype and cast methods
- 1mo agovecvecALTREP vectors survive construction and printing intact
- 3mo agovecvecThe class is rebuilt on S7, with a new internal representation ⚡
- 4mo agovecvecMissing value handling fixed for is.na()
- 11mo agovecvecArithmetic and per-vector apply arrive
- 11mo agovecvecFirst release: constructors and vctrs dispatch
- 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 vecvec?
Both compete on the same themes — r-package — within Analytics. GeneNMF and vecvec 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 vecvec?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and vecvec 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 vecvec?
Top vecvec alternatives in Analytics are ranked by recent ship velocity. Browse the "vecvec alternatives" section above for the current picks, or visit /alternatives/vecvec for the full list with editorial commentary on each.