STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs washdata
A side-by-side editorial comparison of GeneNMF and washdata — release velocity, themes, recent moves, and the top alternatives to consider.
GeneNMF vs washdata: 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 washdata?
washdata is a fixed survey dataset; eight years of releases have changed only its packaging.
A data package distributing the Urban Water and Sanitation Survey, on CRAN since January 2018. No release has altered the data. The 2018 pair added survey country, year and aim to DESCRIPTION and fixed a README link; everything since — 2020, 2024 and the January 2026 release — is documentation, formatting, badges, repository refreshes and updates for a new rhub version.
GeneNMF vs washdata: 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.
washdata
0.0ANALYTICS
washdata is a fixed survey dataset; eight years of releases have changed only its packaging.
◆ Current state
A data package distributing the Urban Water and Sanitation Survey, on CRAN since January 2018. No release has altered the data. The 2018 pair added survey country, year and aim to DESCRIPTION and fixed a README link; everything since — 2020, 2024 and the January 2026 release — is documentation, formatting, badges, repository refreshes and updates for a new rhub version.
◆ Where it's heading
Nothing is heading anywhere, and for a dataset package that is the point: the value is a citable, unchanging artifact, and the release history exists to keep it installable as R's toolchain moves. The maintenance cadence matches the maintainer's other nutrition packages, which received the same repository-refresh treatment in the same period. Note also that the tags are backfilled out of order — v0.1.0 carries a later stamp than v0.1.2.
◆ Prediction
Expect further releases only when CRAN checks or infrastructure require them; there is no indication the survey data itself will be extended.
Alternatives to GeneNMF and washdata
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 washdata.
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 washdata alternatives →
Recent activity from GeneNMF and washdata
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 6mo agowashdataRepository and toolchain maintenance
- 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 agowashdataDocumentation and formatting updates
- 2y agoGeneNMFFirst stable release published to CRAN
- 5y agowashdataSecond release: documentation and formatting
- 8y agowashdataPre-release of the survey dataset
- 8y agowashdataFirst CRAN release of the Urban Water and Sanitation Survey
Frequently asked questions
What is the difference between GeneNMF and washdata?
They serve adjacent needs but don't currently overlap on shipped themes. GeneNMF and washdata 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 washdata?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and washdata 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 washdata?
Top washdata alternatives in Analytics are ranked by recent ship velocity. Browse the "washdata alternatives" section above for the current picks, or visit /alternatives/washdata for the full list with editorial commentary on each.