STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs hoopr
A side-by-side editorial comparison of GeneNMF and hoopr — release velocity, themes, recent moves, and the top alternatives to consider.
GeneNMF vs hoopr: 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 hoopr?
hoopR rebuilds its HTTP layer on httr2 to stop segfaulting on modern systems
hoopR is the sportsdataverse R package for basketball data, wrapping ESPN, NBA Stats, NBA G-League, NCAA and KenPom behind a single set of loaders. Version 3.0.0 replaces httr with httr2 across every one of those backends, drops httr from Imports, and routes all calls through shared internal retry and response helpers. The change is breaking, and it exists because the old stack segfaulted against libcurl 8.x and curl 7.0.0.
GeneNMF vs hoopr: 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.
hoopr
0.0ANALYTICS
hoopR rebuilds its HTTP layer on httr2 to stop segfaulting on modern systems
◆ Current state
hoopR is the sportsdataverse R package for basketball data, wrapping ESPN, NBA Stats, NBA G-League, NCAA and KenPom behind a single set of loaders. Version 3.0.0 replaces httr with httr2 across every one of those backends, drops httr from Imports, and routes all calls through shared internal retry and response helpers. The change is breaking, and it exists because the old stack segfaulted against libcurl 8.x and curl 7.0.0.
◆ Where it's heading
The package's history is two distinct eras. Through 2021-2023 it grew by endpoint accretion — ESPN stat functions, G-League coverage, the NBA live and boxscore V3 families, on-court players in play-by-play — expanding what could be pulled. The recent work is consolidation instead: one HTTP pipeline, one messaging library, data served from the shared sportsdataverse-data releases rather than per-package repositories. The centre of gravity has moved from adding endpoints to making the plumbing survive its dependencies.
◆ Prediction
With the HTTP layer unified behind shared helpers, expect the sibling sportsdataverse packages to follow the same httr2 migration, and hoopR's own next releases to resume endpoint work now that requests run through one pipeline.
Alternatives to GeneNMF and hoopr
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 hoopr.
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 hoopr alternatives →
Recent activity from GeneNMF and hoopr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 4mo agohooprhoopR 3.0.0 moves every API backend to httr2 ⚡
- 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
- 2y agohooprData loaders repoint to sportsdataverse-data; NBA live endpoints
- 4y agohooprESPN stat functions and G-League coverage added
- 4y agohooprCRAN release with documented return shapes
- 4y agohooprhoopR 1.4.4
- 4y agohooprhoopR 1.4.3
Frequently asked questions
What is the difference between GeneNMF and hoopr?
They serve adjacent needs but don't currently overlap on shipped themes. GeneNMF and hoopr 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 hoopr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and hoopr 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 hoopr?
Top hoopr alternatives in Analytics are ranked by recent ship velocity. Browse the "hoopr alternatives" section above for the current picks, or visit /alternatives/hoopr for the full list with editorial commentary on each.