STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs r-owidapi
A side-by-side editorial comparison of GeneNMF and r-owidapi — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs r-owidapi: 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 r-owidapi?
The R client for Our World in Data found its search had been reading a tenth of the catalog.
owidapi is a small R client for Our World in Data, covering chart data retrieval, metadata, the full chart catalog, and search over it, with experimental Shiny output helpers. It is three releases old and the most recent one is almost entirely repair: the catalog function was silently truncating at 1000 rows because of a Datasette row cap, which meant search had been operating on a fraction of what exists.
GeneNMF vs r-owidapi: 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.
r-owidapi
2.5ANALYTICS
The R client for Our World in Data found its search had been reading a tenth of the catalog.
◆ Current state
owidapi is a small R client for Our World in Data, covering chart data retrieval, metadata, the full chart catalog, and search over it, with experimental Shiny output helpers. It is three releases old and the most recent one is almost entirely repair: the catalog function was silently truncating at 1000 rows because of a Datasette row cap, which meant search had been operating on a fraction of what exists.
◆ Where it's heading
Development is about making a thin wrapper trustworthy against an upstream that moves without notice. The truncation fix pages through the catalog properly; a separate fix stops the function breaking when Our World in Data dropped a column, by parsing typed columns only when present. Tests moved to mocked responses, with a small live suite retained purely to detect schema drift and skipped on CRAN — a sensible design for a package whose main risk is that the API changes shape rather than that the code is wrong. The user-facing surface has not grown since the initial release; the work is in defending it.
◆ Prediction
On this pattern the next release is likelier to be another upstream-compatibility fix than new functionality, with the schema-drift tests the mechanism that surfaces it.
Alternatives to GeneNMF and r-owidapi
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 r-owidapi.
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 r-owidapi alternatives →
Recent activity from GeneNMF and r-owidapi
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 20d agor-owidapiCatalog was silently capped at 1000 charts; now paged in full
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agor-owidapiRequest logic consolidated, with graceful catalog errors
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agor-owidapiFirst release: data, metadata, catalog and search
- 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 r-owidapi?
Both compete on the same themes — r-package — within Analytics. r-owidapi is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is GeneNMF better than r-owidapi?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. r-owidapi is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. 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 r-owidapi?
Top r-owidapi alternatives in Analytics are ranked by recent ship velocity. Browse the "r-owidapi alternatives" section above for the current picks, or visit /alternatives/r-owidapi for the full list with editorial commentary on each.