STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
forecasting vs GeneNMF
A side-by-side editorial comparison of forecasting and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
forecasting vs GeneNMF: at a glance
What is forecasting?
HIDDA.forecasting is a book chapter's reproducibility artifact, not a package under development.
HIDDA.forecasting accompanies a book chapter on forecasting infectious disease counts; its vignettes reproduce the results presented there using arima, prophet, glarma, hhh4contacts and scoringRules. The 1.0.0 release states this outright — it is the version used for the chapter, pinned to CRAN package versions as of July 2018. Every release since has been a vignette rebuild against newer R and dependency versions.
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.
forecasting vs GeneNMF: editorial side-by-side
forecasting
0.0ANALYTICS
HIDDA.forecasting is a book chapter's reproducibility artifact, not a package under development.
◆ Current state
HIDDA.forecasting accompanies a book chapter on forecasting infectious disease counts; its vignettes reproduce the results presented there using arima, prophet, glarma, hhh4contacts and scoringRules. The 1.0.0 release states this outright — it is the version used for the chapter, pinned to CRAN package versions as of July 2018. Every release since has been a vignette rebuild against newer R and dependency versions.
◆ Where it's heading
The release pattern is maintenance on an eight-year cadence dictated entirely by the surrounding ecosystem: 1.1.1 rebuilt under R 4.0.4, 1.1.2 under R 4.3.2, 1.1.3 under R 4.6.1, each reporting whether the numbers moved. They mostly have not — the recurring note is minor numerical differences confined to the prophet forecasts in vignette('CHILI_prophet'). The only substantive change in the visible history is 1.1.0's methodological tidy-up of the scoring comparisons.
◆ Prediction
Nothing in these entries points to new functionality; the next release is most likely another vignette rebuild whenever a dependency change or a CRAN check failure forces one.
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 forecasting 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 forecasting 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 forecasting alternatives → · See all GeneNMF alternatives →
Recent activity from forecasting and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agoforecastingVignettes rebuilt under R 4.6.1
- 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
- 2y agoforecastingVignettes rebuilt under R 4.3.2
- 5y agoforecastingVignettes rebuilt under R 4.0.4
- 7y agoforecastingStandard PIT and discretized log-normal scoring
- 7y agoforecastingThe version used for the book chapter, with pinned dependencies
Frequently asked questions
What is the difference between forecasting and GeneNMF?
They serve adjacent needs but don't currently overlap on shipped themes. forecasting 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 forecasting better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. forecasting 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 forecasting?
Top forecasting alternatives in Analytics are ranked by recent ship velocity. Browse the "forecasting alternatives" section above for the current picks, or visit /alternatives/forecasting 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.