STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
fracture vs GeneNMF
A side-by-side editorial comparison of fracture and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
fracture vs GeneNMF: at a glance
What is fracture?
fracture solved decimal-to-fraction conversion years ago and now only answers to CRAN.
A single-purpose package converting decimals to fractions, with a matrix form and a Unicode pretty-printer. The functional work finished in 2021-2022: an explicit denom argument, named-argument-only calling, sensible denominators at 0 and 1, and NA and Inf handled rather than erroring. The only release since is a four-year-later removal of a C++11 system requirement that R's C++17 default made redundant.
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.
fracture vs GeneNMF: editorial side-by-side
fracture
0.0ANALYTICS
fracture solved decimal-to-fraction conversion years ago and now only answers to CRAN.
◆ Current state
A single-purpose package converting decimals to fractions, with a matrix form and a Unicode pretty-printer. The functional work finished in 2021-2022: an explicit denom argument, named-argument-only calling, sensible denominators at 0 and 1, and NA and Inf handled rather than erroring. The only release since is a four-year-later removal of a C++11 system requirement that R's C++17 default made redundant.
◆ Where it's heading
This is a completed utility. Its arc ran from correctness — floating-point rounding, exhaustive tests across millions of fractions — through API tightening, to edge-case tolerance, and then stopped. The 2026 release contains no user-visible change at all; it exists because CRAN's toolchain moved, which is the characteristic maintenance mode of a small package that does one thing correctly.
◆ Prediction
Nothing in these entries suggests new functionality; expect further releases only when R or CRAN policy forces one, as this one did.
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 fracture 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 fracture 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 fracture alternatives → · See all GeneNMF alternatives →
Recent activity from fracture and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 6mo agofractureObsolete C++11 requirement removed
- 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
- 4y agofractureNA and Inf inputs handled instead of erroring
- 4y agofractureExplicit denominator argument; arguments now named-only
- 5y agofractureUnicode fraction formatting and rounding fixes
Frequently asked questions
What is the difference between fracture and GeneNMF?
They serve adjacent needs but don't currently overlap on shipped themes. fracture 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 fracture better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. fracture 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 fracture?
Top fracture alternatives in Analytics are ranked by recent ship velocity. Browse the "fracture alternatives" section above for the current picks, or visit /alternatives/fracture 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.