roclang
A roxygen2 documentation-reuse helper whose release notes are mostly upstream damage control.
Comparison · Analytics
firatheme vs GeneNMF
A side-by-side editorial comparison of firatheme and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
firatheme vs GeneNMF: at a glance
What is firatheme?
firatheme woke up after four years and started fixing what ggplot2 changed underneath it.
A ggplot2 theme built around the Fira font family. It went quiet after the 2021 releases that made it pass R CMD check cleanly on all three platforms, then returned in December 2025 with a maintenance release solving a ggplot2 deprecation warning and cleaning up text alignment, followed six weeks later by a facet argument to theme_fira() that adds borders and a custom strip background so facet labels stay legible.
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.
firatheme vs GeneNMF: editorial side-by-side
firatheme
0.0ANALYTICS
firatheme woke up after four years and started fixing what ggplot2 changed underneath it.
◆ Current state
A ggplot2 theme built around the Fira font family. It went quiet after the 2021 releases that made it pass R CMD check cleanly on all three platforms, then returned in December 2025 with a maintenance release solving a ggplot2 deprecation warning and cleaning up text alignment, followed six weeks later by a facet argument to theme_fira() that adds borders and a custom strip background so facet labels stay legible.
◆ Where it's heading
The pattern of the revival is compatibility first, then the gap users actually hit. Faceting is the obvious hole in any hand-built theme — strip labels are where a theme that looks right on a single panel falls apart — and it arrived immediately after the deprecation cleanup, from a new contributor who has now made every recent change. Note the 0.2.4 release notes restate 0.2.3's contents rather than describing new work.
◆ Prediction
With faceting handled, further releases most likely track ggplot2 deprecations; the entries don't support a stronger claim than that.
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.
Alternatives to firatheme and GeneNMF
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 firatheme or GeneNMF.
gratia
The tidy front-end for GAMs, now stable enough that upstream ggplot2 sets its release calendar.
incase
A safer case_when that keeps hardening its guarantees while realigning to tidyverse naming.
reda
A mature recurrent-event toolkit in careful maintenance, shedding weight rather than adding surface.
TidyDensity
A distribution catalogue that grows by one family at a time, and rarely breaks anything.
cfbfastr
College football's open data client hit v2 — and now reports how many API calls you have left.
See all firatheme alternatives → · See all GeneNMF alternatives →
Recent activity from firatheme and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 7mo agofirathemeFaceting support with borders and custom strips
- 8mo agofirathemeText alignment cleanup and ggplot2 deprecation fix
- 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
- 5y agofirathemeClean builds across all three platforms
- 5y agofirathemetheme_fira no longer returns a list
- 6y agofirathemeInitial citable release
Frequently asked questions
What is the difference between firatheme and GeneNMF?
They serve adjacent needs but don't currently overlap on shipped themes. firatheme and GeneNMF 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 firatheme better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. firatheme and GeneNMF 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 firatheme?
Top firatheme alternatives in Analytics are ranked by recent ship velocity. Browse the "firatheme alternatives" section above for the current picks, or visit /alternatives/firatheme for the full list with editorial commentary on each.
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.