nat.nblast
The NBLAST neuron-similarity engine is stable code on life support, shipping once every few years.
Comparison · Analytics
GeneNMF vs haze
A side-by-side editorial comparison of GeneNMF and haze — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs haze: 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 haze?
Four dormant years end with a modernization pass and an off-by-one fix in the C++ core
haze does nearest-neighbour smoothing and k-d tree interpolation on brain surface meshes. It sat untouched from April 2022 until July 2026, when a single release modernized it for current R versions and corrected an off-by-one error in the C++ code. It is not on CRAN and never will be — the package exceeds 50MB against CRAN's 5MB ceiling, a constraint its own initial release notes acknowledge.
GeneNMF vs haze: 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.
haze
2.5ANALYTICS
Four dormant years end with a modernization pass and an off-by-one fix in the C++ core
◆ Current state
haze does nearest-neighbour smoothing and k-d tree interpolation on brain surface meshes. It sat untouched from April 2022 until July 2026, when a single release modernized it for current R versions and corrected an off-by-one error in the C++ code. It is not on CRAN and never will be — the package exceeds 50MB against CRAN's 5MB ceiling, a constraint its own initial release notes acknowledge.
◆ Where it's heading
The July 2026 release arrived 56 minutes after its sibling regfusionr 0.3.0 from the same maintainer, which is the tell: this is a maintainer sweeping a set of related neuroimaging packages back into working order, not independent development on haze itself. haze is the dependency, regfusionr the consumer, and the substantive work sits on the regfusionr side. The off-by-one correction is the only change here that alters results.
◆ Prediction
Expect haze to move only when a downstream dfsp-spirit package needs it to — its cadence is driven by the sibling packages, not by its own roadmap.
Alternatives to GeneNMF and haze
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 haze.
RandomWalker
A random-walk generator that outgrew one dimension and renamed its core column to prove it.
tbrf
Time-based rolling statistics for water-quality data, finally getting plotting and padding built in.
roclang
A roxygen2 documentation-reuse helper whose release notes are mostly upstream damage control.
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.
See all GeneNMF alternatives → · See all haze alternatives →
Recent activity from GeneNMF and haze
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 18d agohazeVersion 0.3.0 -- Fixes and modernization
- 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
- 4y agohazev0.2.0 -- kdtrees
- 4y agohazev0.1.0: Initial release
Frequently asked questions
What is the difference between GeneNMF and haze?
Both compete on the same themes — r-package — within Analytics. haze is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 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 haze?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. haze is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 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 haze?
Top haze alternatives in Analytics are ranked by recent ship velocity. Browse the "haze alternatives" section above for the current picks, or visit /alternatives/haze for the full list with editorial commentary on each.