STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs rempsyc
A side-by-side editorial comparison of GeneNMF and rempsyc — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs rempsyc: 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 rempsyc?
Publication-ready psychology tables and plots, tracking APA style as closely as the software allows.
rempsyc produces APA-formatted tables and figures for psychology research — nice_table() for results tables, plus plotting helpers for scatter plots, violin plots, densities and simple slopes. Its releases are CRAN submissions that bundle a long run of development versions, so each entry reads as a digest rather than a single change. The most recent, 0.2.0, added point labelling and per-group correlation statistics to nice_scatter and fixed nice_lm() failing on factor covariates with more than two levels.
GeneNMF vs rempsyc: 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.
rempsyc
0.0ANALYTICS
Publication-ready psychology tables and plots, tracking APA style as closely as the software allows.
◆ Current state
rempsyc produces APA-formatted tables and figures for psychology research — nice_table() for results tables, plus plotting helpers for scatter plots, violin plots, densities and simple slopes. Its releases are CRAN submissions that bundle a long run of development versions, so each entry reads as a digest rather than a single change. The most recent, 0.2.0, added point labelling and per-group correlation statistics to nice_scatter and fixed nice_lm() failing on factor covariates with more than two levels.
◆ Where it's heading
Two forces drive this package and neither is its own roadmap. The first is APA style: when the 7th edition advised against beta for standardized coefficients, the package switched its output to italic b with an asterisk. The second is the surrounding ecosystem — formatting is aligned to what lavaanExtra and afex produce, contrast handling was delegated to easystats' modelbased, and Excel correlation matrix export was handed entirely to the correlation package to cut maintenance.
◆ Prediction
The pattern of delegating functionality to specialist packages while keeping the formatting layer is well established and likely continues. Because releases bundle many small dev versions, the next one will probably again mix plotting refinements with fixes surfaced by upstream changes.
Alternatives to GeneNMF and rempsyc
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 rempsyc.
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 rempsyc alternatives →
Recent activity from GeneNMF and rempsyc
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 11mo agorempsycPoint labels and per-group correlations added to nice_scatter
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agorempsycExcel correlation export delegated to the correlation package
- 1y agoGeneNMFSimilarity heatmap downsampling and meta-program removal
- 2y agoGeneNMFMeta-programs rebuilt on gene weight vectors and cosine similarity ⚡
- 2y agorempsycTable spacing control and a fix for name collision with afex
- 2y agoGeneNMFFirst stable release published to CRAN
- 2y agorempsycStandardized coefficients switch to APA 7th edition b* notation
- 2y agorempsycLegend and standardization-check fixes
- 2y agorempsycnice_table starts coercing model objects automatically
Frequently asked questions
What is the difference between GeneNMF and rempsyc?
Both compete on the same themes — r-package — within Analytics. GeneNMF and rempsyc 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 rempsyc?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and rempsyc 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 rempsyc?
Top rempsyc alternatives in Analytics are ranked by recent ship velocity. Browse the "rempsyc alternatives" section above for the current picks, or visit /alternatives/rempsyc for the full list with editorial commentary on each.