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Comparison · Analytics
GeneNMF vs nswgeo
A side-by-side editorial comparison of GeneNMF and nswgeo — release velocity, themes, recent moves, and the top alternatives to consider.
GeneNMF vs nswgeo: 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 nswgeo?
NSW boundary data for R, refreshed as the official sources move
nswgeo packages New South Wales geographic boundaries for R — suburbs, postcodes, local government areas, Primary Health Networks and Local Health Districts — as ready-to-plot sf datasets. The 0.6.0 release refreshes nearly all of them against new upstream sources, moving postcodes to 2021 ABS boundaries and taking LHD boundaries from a new official feed. It is maintained by cidm-ph alongside the mapping packages that consume it, including ggmapinset.
GeneNMF vs nswgeo: 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.
nswgeo
0.0ANALYTICS
NSW boundary data for R, refreshed as the official sources move
◆ Current state
nswgeo packages New South Wales geographic boundaries for R — suburbs, postcodes, local government areas, Primary Health Networks and Local Health Districts — as ready-to-plot sf datasets. The 0.6.0 release refreshes nearly all of them against new upstream sources, moving postcodes to 2021 ABS boundaries and taking LHD boundaries from a new official feed. It is maintained by cidm-ph alongside the mapping packages that consume it, including ggmapinset.
◆ Where it's heading
Every release is dictated by an upstream release calendar rather than a roadmap: the 2023 ASGS, then 2024, then the 2021 ABS postcode boundaries and the new LHD source. That makes field-name churn the package's defining hazard — LGA_NAME_2021 to LGA_NAME_2023 to LGA_NAME_2024, and now lhd_name carrying a Local Health District suffix. The maintainer's habit of registering compatibility aliases through cartographer shows an awareness that these renames break downstream code silently.
◆ Prediction
Expect the next release to track the following ASGS edition with another round of field renames, and any new content to stay in the health-geography area the package's users work in.
Alternatives to GeneNMF and nswgeo
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 nswgeo.
cfbfastr
College football's open data client hit v2 — and now reports how many API calls you have left.
rnpn
The USA phenology data client rebuilt its entire stack and stopped handing users -9999 as a number.
rempsyc
Publication-ready psychology tables and plots, tracking APA style as closely as the software allows.
sdsfun
A spatial-statistics utility package exists to be depended on, and is built accordingly.
eulerr
The area-proportional Euler diagram package is finished software, and maintained like it.
See all GeneNMF alternatives → · See all nswgeo alternatives →
Recent activity from GeneNMF and nswgeo
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 4mo agonswgeoSuburb, postcode, PHN and LHD boundaries all refreshed
- 6mo agonswgeonswgeo 0.5.1
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agonswgeoUpdated to the 2024 ASGS release
- 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 agonswgeoTerritories, PHN maps and the outline() helper added
Frequently asked questions
What is the difference between GeneNMF and nswgeo?
They serve adjacent needs but don't currently overlap on shipped themes. GeneNMF and nswgeo 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 nswgeo?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and nswgeo 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 nswgeo?
Top nswgeo alternatives in Analytics are ranked by recent ship velocity. Browse the "nswgeo alternatives" section above for the current picks, or visit /alternatives/nswgeo for the full list with editorial commentary on each.