roclang
A roxygen2 documentation-reuse helper whose release notes are mostly upstream damage control.
Comparison · Analytics
GeneNMF vs rmediation
A side-by-side editorial comparison of GeneNMF and rmediation — release velocity, themes, recent moves, and the top alternatives to consider.
GeneNMF vs rmediation: 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 rmediation?
RMediation shipped a three-normal CDF, then found it was silently wrong.
RMediation is a long-standing CRAN package for confidence intervals on mediated effects, now built on an S7 class hierarchy. Over eight weeks it added ProductNormal3 for serial indirect effects of the form a1*a2*b, folded the engine into the existing pprodnormal naming family, and then replaced that engine outright after finding it returned wrong probabilities without warning. The dev branch is at 1.7.0; CRAN still serves 1.6.1.
GeneNMF vs rmediation: 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.
rmediation
3.8ANALYTICS
RMediation shipped a three-normal CDF, then found it was silently wrong.
◆ Current state
RMediation is a long-standing CRAN package for confidence intervals on mediated effects, now built on an S7 class hierarchy. Over eight weeks it added ProductNormal3 for serial indirect effects of the form a1*a2*b, folded the engine into the existing pprodnormal naming family, and then replaced that engine outright after finding it returned wrong probabilities without warning. The dev branch is at 1.7.0; CRAN still serves 1.6.1.
◆ Where it's heading
The package is moving from a hand-rolled numerical layer to one that checks itself: the new default integrator escalates its node count until successive rules agree, warns when it hits the cap instead of returning a number, and exposes a diagnostics argument for the convergence estimate. The correctness fix went to dev ahead of the CRAN window rather than being held for it, which suggests wrong-answer bugs are treated as release-blocking regardless of cadence. Serial mediation is where the new surface area is concentrated.
◆ Prediction
1.7.0 exists specifically to land before CRAN's 2026-08-21 update window, so the next move is a CRAN submission promoting it to main; whether hcubature survives past that as a cross-check option is the open question.
Alternatives to GeneNMF and rmediation
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 rmediation.
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 GeneNMF alternatives → · See all rmediation alternatives →
Recent activity from GeneNMF and rmediation
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 14h agormediationv1.7.0 — pprodnormal3() correctness fix ⚡
- 1mo agormediationp_prod3() renamed into the pprodnormal family
- 1mo agormediationProductNormal3: exact CDF for a product of three normals ⚡
- 2mo agormediationmedfit reaches CRAN; Remotes pointer dropped
- 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 rmediation?
They serve adjacent needs but don't currently overlap on shipped themes. rmediation 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 rmediation?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. rmediation 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 rmediation?
Top rmediation alternatives in Analytics are ranked by recent ship velocity. Browse the "rmediation alternatives" section above for the current picks, or visit /alternatives/rmediation for the full list with editorial commentary on each.