STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs reliaplotr
A side-by-side editorial comparison of GeneNMF and reliaplotr — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs reliaplotr: 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 reliaplotr?
The Weibull plotting package renamed itself, then handed its charts to AI assistants.
ReliaPlotR draws interactive reliability plots with plotly — probability plots, contour plots, Duane and reliability growth charts, accelerated life testing plots by stress level, mean cumulative function curves for repairable systems, and exposure plots. It was WeibullR.plotly until late 2025, and the rename tracked a real widening of scope rather than just a label change. The current release adds tidy extractors that turn fitted model objects into data frames, and an MCP server exposing five of its fit and plot functions as tools.
GeneNMF vs reliaplotr: 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.
reliaplotr
0.0ANALYTICS
The Weibull plotting package renamed itself, then handed its charts to AI assistants.
◆ Current state
ReliaPlotR draws interactive reliability plots with plotly — probability plots, contour plots, Duane and reliability growth charts, accelerated life testing plots by stress level, mean cumulative function curves for repairable systems, and exposure plots. It was WeibullR.plotly until late 2025, and the rename tracked a real widening of scope rather than just a label change. The current release adds tidy extractors that turn fitted model objects into data frames, and an MCP server exposing five of its fit and plot functions as tools.
◆ Where it's heading
The package has been following its analysis siblings function for function: as accelerated life testing and repairable systems modelling landed in the wider suite, the matching plot types appeared here, and when the growth-analysis package shipped an MCP server, this one followed two weeks later. The tidy extractors point the same way — a plotting package that can also return parameter estimates, goodness-of-fit metrics, and confidence bounds as tidy frames is one designed to be consumed programmatically, by a pipeline or an assistant, not only read on screen. Overlaying multiple model fits on a single plot has been a recurring request answered across several releases.
◆ Prediction
Expect the tidy extractor and MCP tool surfaces to keep expanding together, since each new plot type in the suite now implies both a chart and a machine-readable version of what it shows.
Alternatives to GeneNMF and reliaplotr
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 reliaplotr.
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 reliaplotr alternatives →
Recent activity from GeneNMF and reliaplotr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 2mo agoreliaplotrTidy model extractors plus five plotting tools over MCP ⚡
- 2mo agoreliaplotrNHPP plots switch to the mean cumulative function
- 4mo agoreliaplotrAccelerated life testing and repairable systems plots added
- 8mo agoreliaplotrDuane plots gain confidence bounds
- 9mo agoreliaplotrReliaPlotR v0.4.1
- 10mo agoreliaplotrRenamed from WeibullR.plotly to ReliaPlotR
- 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 reliaplotr?
Both compete on the same themes — r-package — within Analytics. GeneNMF and reliaplotr 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 reliaplotr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and reliaplotr 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 reliaplotr?
Top reliaplotr alternatives in Analytics are ranked by recent ship velocity. Browse the "reliaplotr alternatives" section above for the current picks, or visit /alternatives/reliaplotr for the full list with editorial commentary on each.