STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs trendseries
A side-by-side editorial comparison of GeneNMF and trendseries — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs trendseries: 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 trendseries?
A trend-extraction toolkit grows a full decomposition engine, seasonal components and all.
trendseries extracts trends from economic time series through two pipe-friendly functions, backed by an unusually broad method set — Hodrick-Prescott in one- and two-sided variants, Baxter-King, Christiano-Fitzgerald, Hamilton regression, Beveridge-Nelson, unobserved components, plus the moving average and smoothing family. The 1.4 release adds decomposition proper: an exported decompose_series() that splits a series into trend, seasonal, and remainder across five methods and guarantees the components add back to the original values.
GeneNMF vs trendseries: 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.
trendseries
3.8ANALYTICS
A trend-extraction toolkit grows a full decomposition engine, seasonal components and all.
◆ Current state
trendseries extracts trends from economic time series through two pipe-friendly functions, backed by an unusually broad method set — Hodrick-Prescott in one- and two-sided variants, Baxter-King, Christiano-Fitzgerald, Hamilton regression, Beveridge-Nelson, unobserved components, plus the moving average and smoothing family. The 1.4 release adds decomposition proper: an exported decompose_series() that splits a series into trend, seasonal, and remainder across five methods and guarantees the components add back to the original values.
◆ Where it's heading
The package is moving from breadth of methods to rigour about what those methods produce. Recent work has been about defaults and guarantees rather than new filters: the unobserved components model now derives its signal-to-noise ratios from Hodrick-Prescott lambdas so the default output is economically interpretable, decomposition carries an exact additive identity, and a log transform gives a uniform multiplicative variant across every method. Naming is being tidied in the same spirit, with group_vars deprecated in favour of group_cols. Side-by-side method comparison — passing several methods and getting each one's components as separate columns — suggests an audience that treats method choice as a research question rather than a setting.
◆ Prediction
Expect the comparison and diagnostic side to keep developing, since the package now produces multiple decompositions of the same series and offers no ranking between them; the entries give no indication of new filters being queued.
Alternatives to GeneNMF and trendseries
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 trendseries.
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 trendseries alternatives →
Recent activity from GeneNMF and trendseries
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 15d agotrendseriesDecomposition becomes a first-class operation, five methods deep ⚡
- 3mo agotrendseriesMulti-column trends and economically grounded UCM defaults
- 10mo agotrendseriesFirst production release with 21 trend extraction methods
- 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 trendseries?
Both compete on the same themes — r-package — within Analytics. trendseries is currently shipping more aggressively (velocity 3.8 vs 0.0), with 1 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 trendseries?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. trendseries is currently shipping more aggressively (velocity 3.8 vs 0.0), with 1 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 trendseries?
Top trendseries alternatives in Analytics are ranked by recent ship velocity. Browse the "trendseries alternatives" section above for the current picks, or visit /alternatives/trendseries for the full list with editorial commentary on each.