STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs mev
A side-by-side editorial comparison of GeneNMF and mev — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs mev: 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 mev?
An extreme-value toolkit reorganised its whole API into prefixed families and tripled its estimator count.
mev provides likelihood-based inference for univariate and multivariate extreme value models — threshold selection, shape estimation, tail dependence and max-stable simulation. Version 2.0 was a deliberate reorganisation: every threshold-selection routine now carries a thselect. prefix, every stability plot a tstab. prefix, and every extremal-dependence measure an xdep. prefix, with the old names deprecated but mostly still working. The same release added a large batch of estimators — Stein-weighted GPD, roughly a dozen shape estimators, second-order regular variation, L-moment GPD and Weissman quantiles.
GeneNMF vs mev: 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.
mev
0.0ANALYTICS
An extreme-value toolkit reorganised its whole API into prefixed families and tripled its estimator count.
◆ Current state
mev provides likelihood-based inference for univariate and multivariate extreme value models — threshold selection, shape estimation, tail dependence and max-stable simulation. Version 2.0 was a deliberate reorganisation: every threshold-selection routine now carries a thselect. prefix, every stability plot a tstab. prefix, and every extremal-dependence measure an xdep. prefix, with the old names deprecated but mostly still working. The same release added a large batch of estimators — Stein-weighted GPD, roughly a dozen shape estimators, second-order regular variation, L-moment GPD and Weissman quantiles.
◆ Where it's heading
The package is consolidating into a reference implementation of the extreme-value literature rather than a collection of one-off routines. Sixteen threshold-selection methods now share standardised arguments and their own plot and print methods with automatic selection, which is the tell: the goal is comparability across methods, not just availability. Dependency reduction runs alongside, with distribution functions written in-package to drop evd and Rsolnp replacing nloptr in earlier releases.
◆ Prediction
Version 2.1 continued adding threshold-selection routines within the new naming scheme, so the next release most likely follows the same pattern — more estimators fitted to the established prefixes, plus fixes to the 2.0 renaming. The entries give no sign of a further structural change.
Alternatives to GeneNMF and mev
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 mev.
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.
Recent activity from GeneNMF and mev
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 9mo agomevTwo more threshold-selection routines slot into the new scheme
- 9mo agomevThreshold, stability and dependence functions regrouped under prefixes ⚡
- 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 agomevBoundary-case likelihood fixes, bundled with the prior release's notes
- 2y agoGeneNMFFirst stable release published to CRAN
- 3y agomevGEV and GP distribution functions brought in-house to drop evd
- 4y agomevFour max-stable families, fixed parameters and threshold diagnostics
Frequently asked questions
What is the difference between GeneNMF and mev?
Both compete on the same themes — r-package — within Analytics. GeneNMF and mev 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 mev?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and mev 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 mev?
Top mev alternatives in Analytics are ranked by recent ship velocity. Browse the "mev alternatives" section above for the current picks, or visit /alternatives/mev for the full list with editorial commentary on each.