STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs ojoregex
A side-by-side editorial comparison of GeneNMF and ojoregex — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs ojoregex: 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 ojoregex?
Oklahoma's court-data nonprofit maintains the regex layer that turns charge text into categories.
ojoregex is Open Justice Oklahoma's pattern library for classifying criminal charge descriptions from court records — the unglamorous translation layer between free-text charge fields and analysable categories. Its entire release history reached this feed as four tags published within three minutes, so the feed order reflects a backfill rather than a shipping cadence. Release notes are merge references rather than descriptions, which limits how much can be read from the changelog alone.
GeneNMF vs ojoregex: 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.
ojoregex
0.0ANALYTICS
Oklahoma's court-data nonprofit maintains the regex layer that turns charge text into categories.
◆ Current state
ojoregex is Open Justice Oklahoma's pattern library for classifying criminal charge descriptions from court records — the unglamorous translation layer between free-text charge fields and analysable categories. Its entire release history reached this feed as four tags published within three minutes, so the feed order reflects a backfill rather than a shipping cadence. Release notes are merge references rather than descriptions, which limits how much can be read from the changelog alone.
◆ Where it's heading
What the notes do show is a package alternating between domain corrections and R tooling upkeep: a fix to property-crime matching in one release, dplyr select semantics in the next. That is the expected shape for a regex catalogue — accuracy work arrives as individual charge types get miscategorised in real analyses, and the rest is keeping the package installable against a moving tidyverse. Contributions come from a small internal team, and the vignette work referenced in the earliest tag suggests the pattern list doubles as documentation for analysts.
◆ Prediction
The visible pattern is incremental match fixes as charge types surface in use; the release notes carry too little detail to predict anything beyond that without reading the underlying pull requests.
Alternatives to GeneNMF and ojoregex
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 ojoregex.
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 ojoregex alternatives →
Recent activity from GeneNMF and ojoregex
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agoojoregexPatch for dplyr select semantics
- 1mo agoojoregexojoregex v0.10.0
- 1mo agoojoregexNamespace prefixes fixed, plus a property-crime match bug
- 1mo agoojoregexFirst tagged release, carrying the whole development history
- 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 ojoregex?
Both compete on the same themes — r-package — within Analytics. GeneNMF and ojoregex 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 ojoregex?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and ojoregex 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 ojoregex?
Top ojoregex alternatives in Analytics are ranked by recent ship velocity. Browse the "ojoregex alternatives" section above for the current picks, or visit /alternatives/ojoregex for the full list with editorial commentary on each.