STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs soilDB
A side-by-side editorial comparison of GeneNMF and soilDB — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs soilDB: 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 soilDB?
The R front door to USDA soil data finishes a long deprecation cleanup and turns local-first.
soilDB is the R access layer for USDA-NRCS soil data: NASIS local databases, Soil Data Access, SoilWeb coverage services, and a widening set of curated national grids. The 2.9.x line closed out a multi-release deprecation cycle — column aliases and stringsAsFactors are gone, R 4.1 is the floor, and the bundled sample profile collections were rebuilt against the new schema. Recent work has shifted from adding query functions to making existing ones faster and usable against local SQLite or GeoPackage copies.
GeneNMF vs soilDB: 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.
soilDB
0.0ANALYTICS
The R front door to USDA soil data finishes a long deprecation cleanup and turns local-first.
◆ Current state
soilDB is the R access layer for USDA-NRCS soil data: NASIS local databases, Soil Data Access, SoilWeb coverage services, and a widening set of curated national grids. The 2.9.x line closed out a multi-release deprecation cycle — column aliases and stringsAsFactors are gone, R 4.1 is the floor, and the bundled sample profile collections were rebuilt against the new schema. Recent work has shifted from adding query functions to making existing ones faster and usable against local SQLite or GeoPackage copies.
◆ Where it's heading
The arc points at offline and local-first workflows. downloadSSURGO() and createSSURGO() keep gaining arguments for building and querying local SSURGO databases, and the query internals were rewritten as common table expressions so identical code runs against the remote service or a local file. Coverage is widening in parallel: FY26 SoilWeb maps now reach most OCONUS surveys, while fetchHWSD() and fetchSOLUS() pull in datasets outside the core NASIS/SSURGO pair. Federal URL churn — EDIT, SoilWeb, S3-hosted geometry — is a recurring maintenance tax the package absorbs on users' behalf.
◆ Prediction
Expect the next releases to keep extending parallel and offline SSURGO handling, since LAPPLY.FUN has just opened the door to arbitrary parallel backends, and to fold more curated SoilWeb and FAO datasets behind fetch* wrappers.
Alternatives to GeneNMF and soilDB
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 soilDB.
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 soilDB alternatives →
Recent activity from GeneNMF and soilDB
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agosoilDBFY26 soil maps reach OCONUS; SSURGO downloads go parallel
- 4mo agosoilDBROSETTA v2 lands as the deprecated NASIS aliases are removed ⚡
- 10mo agosoilDBNASIS record IDs now retrievable through Soil Data Access
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 11mo agosoilDBSpatial queries can pull columns from non-spatial tables
- 1y agosoilDBNASIS 7.4.3 metadata, plus HWSD and a local cache in 2.8.10
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agosoilDBQuery internals rewritten as CTEs for local SQLite support
- 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 soilDB?
Both compete on the same themes — r-package — within Analytics. GeneNMF and soilDB 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 soilDB?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and soilDB 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 soilDB?
Top soilDB alternatives in Analytics are ranked by recent ship velocity. Browse the "soilDB alternatives" section above for the current picks, or visit /alternatives/soildb for the full list with editorial commentary on each.