STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
arcgisutils vs GeneNMF
A side-by-side editorial comparison of arcgisutils and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
arcgisutils vs GeneNMF: at a glance
What is arcgisutils?
The R-ArcGIS plumbing layer grew a portal administration API and geoprocessing job support.
arcgisutils is the foundation of the R interface to ArcGIS — token handling, standardized httr2 request construction, and conversion between Esri JSON and R types for the packages built on top of it. Version 0.4.0 in October 2025 broadened it well past that role, adding functions to enumerate a portal's federated servers, users and resources, search content with automatic pagination, and submit geoprocessing jobs through new S7 classes. Token management has been on its current footing since 0.2.0, which moved tokens into an internal environment supporting multiple named keys.
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.
arcgisutils vs GeneNMF: editorial side-by-side
arcgisutils
0.0ANALYTICS
The R-ArcGIS plumbing layer grew a portal administration API and geoprocessing job support.
◆ Current state
arcgisutils is the foundation of the R interface to ArcGIS — token handling, standardized httr2 request construction, and conversion between Esri JSON and R types for the packages built on top of it. Version 0.4.0 in October 2025 broadened it well past that role, adding functions to enumerate a portal's federated servers, users and resources, search content with automatic pagination, and submit geoprocessing jobs through new S7 classes. Token management has been on its current footing since 0.2.0, which moved tokens into an internal environment supporting multiple named keys.
◆ Where it's heading
The package is expanding from request plumbing into direct coverage of the ArcGIS Enterprise administrative and geoprocessing surface, which is a different kind of work from what it existed to support. Much of the new surface is marked experimental, so the shape is still being settled. Alongside the expansion runs steady API tidying — three deprecations and two functions removed outright in the same release, one of which dropped the dbplyr dependency.
◆ Prediction
The experimental sharing-API and URL-parsing functions are the most likely to change or firm up next, and the geoprocessing classes suggest job execution will be built out further. Given this package sits beneath arcgislayers, the deprecations introduced here will need a corresponding pass downstream.
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 arcgisutils 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 arcgisutils or GeneNMF.
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 arcgisutils alternatives → · See all GeneNMF alternatives →
Recent activity from arcgisutils and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 10mo agoarcgisutilsPortal administration and geoprocessing jobs join the utility layer ⚡
- 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
- 1y agoarcgisutilsIntegers no longer encoded as floats in feature updates
- 2y agoGeneNMFMeta-programs rebuilt on gene weight vectors and cosine similarity ⚡
- 2y agoGeneNMFFirst stable release published to CRAN
- 2y agoarcgisutilsFirst stable release rebuilds token handling around a token store
Frequently asked questions
What is the difference between arcgisutils and GeneNMF?
Both compete on the same themes — r-package — within Analytics. arcgisutils 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 arcgisutils better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. arcgisutils 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 arcgisutils?
Top arcgisutils alternatives in Analytics are ranked by recent ship velocity. Browse the "arcgisutils alternatives" section above for the current picks, or visit /alternatives/arcgisutils 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.