STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs tEDM
A side-by-side editorial comparison of GeneNMF and tEDM — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs tEDM: 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 tEDM?
The temporal half of the stscl EDM pair, tracking its spatial sibling
tEDM applies empirical dynamic modeling to time series — cross mapping, convergent cross mapping and the logistic map — as the temporal counterpart to spEDM, with which it shares a maintainer and a C++ core. The recent releases are consolidation rather than expansion: index handling in cross mapping corrected, generics taught to accept varying E, k and tau, and the associated paper now cited in the README. Only three releases are visible in the feed.
GeneNMF vs tEDM: 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.
tEDM
0.0ANALYTICS
The temporal half of the stscl EDM pair, tracking its spatial sibling
◆ Current state
tEDM applies empirical dynamic modeling to time series — cross mapping, convergent cross mapping and the logistic map — as the temporal counterpart to spEDM, with which it shares a maintainer and a C++ core. The recent releases are consolidation rather than expansion: index handling in cross mapping corrected, generics taught to accept varying E, k and tau, and the associated paper now cited in the README. Only three releases are visible in the feed.
◆ Where it's heading
tEDM moves in lockstep with spEDM. Configurable distance metrics, varying E/k/tau inputs, strict floating-point comparison and the S3 plotting font unification all appear in both packages within days or weeks, as does the maintainer surname correction. The recent balance has tilted toward correcting library and prediction index handling — the kind of repeated attention that suggests the indexing model was the weak point of the shared core.
◆ Prediction
Expect tEDM to keep inheriting the shared-core changes spEDM lands, with its own releases staying small and centred on cross-mapping parameter handling rather than new method surface.
Alternatives to GeneNMF and tEDM
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 tEDM.
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 tEDM alternatives →
Recent activity from GeneNMF and tEDM
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 4mo agotEDMMaintainer name corrected, published paper cited
- 7mo agotEDMCross-mapping index handling corrected, generics accept varying E, k, tau
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 11mo agotEDMConfigurable distance metrics for cross mapping
- 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 tEDM?
Both compete on the same themes — r-package — within Analytics. GeneNMF and tEDM 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 tEDM?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and tEDM 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 tEDM?
Top tEDM alternatives in Analytics are ranked by recent ship velocity. Browse the "tEDM alternatives" section above for the current picks, or visit /alternatives/tedm for the full list with editorial commentary on each.