STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs hydroloom
A side-by-side editorial comparison of GeneNMF and hydroloom — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs hydroloom: 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 hydroloom?
USGS puts a type system over its river network toolkit so errors surface at dispatch
hydroloom builds and navigates hydrologic flow networks, carrying functionality migrated out of nhdplusTools. Version 1.2.0 introduces an S3 class hierarchy — hy_topo, hy_leveled, hy_node, hy_flownetwork — assigned automatically by hy() and by producer functions, letting the package validate input at dispatch time and emit guided errors. Outlet detection is now defined explicitly: a row is an outlet when its toid is not in id, with reserved values, NA and implicit absence all accepted.
GeneNMF vs hydroloom: 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.
hydroloom
0.0ANALYTICS
USGS puts a type system over its river network toolkit so errors surface at dispatch
◆ Current state
hydroloom builds and navigates hydrologic flow networks, carrying functionality migrated out of nhdplusTools. Version 1.2.0 introduces an S3 class hierarchy — hy_topo, hy_leveled, hy_node, hy_flownetwork — assigned automatically by hy() and by producer functions, letting the package validate input at dispatch time and emit guided errors. Outlet detection is now defined explicitly: a row is an outlet when its toid is not in id, with reserved values, NA and implicit absence all accepted.
◆ Where it's heading
The package spent its first releases porting and broadening — non-dendritic network support, divergence routing, subsetting that follows diversions out of a basin — and has now turned to making that surface safe to use. The class hierarchy is the structural expression of that turn: instead of every function re-checking whether a data frame has the columns it needs, the type carries the guarantee. The explicit outlet rule resolves a category of failure where valid networks errored on NA or orphan toid values.
◆ Prediction
The release notes flag that subclass attributes are stripped by standard dplyr operations, which is the kind of rough edge that usually generates follow-up work — expect attribute preservation or restoration helpers next.
Alternatives to GeneNMF and hydroloom
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 hydroloom.
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 hydroloom alternatives →
Recent activity from GeneNMF and hydroloom
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 2mo agohydroloomhydroloom v1.2.0 ⚡
- 5mo agohydroloomTest tolerances relaxed for CRAN Fedora checks
- 5mo agohydroloomNetwork subsetting and divergence-routed accumulation
- 10mo agohydroloomSort and indexing fixes
- 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 agohydroloomUpmain and downmain navigation for non-dendritic networks
- 2y agoGeneNMFMeta-programs rebuilt on gene weight vectors and cosine similarity ⚡
- 2y agoGeneNMFFirst stable release published to CRAN
- 2y agohydroloomInitial release completing the nhdplusTools migration
Frequently asked questions
What is the difference between GeneNMF and hydroloom?
Both compete on the same themes — r-package — within Analytics. GeneNMF and hydroloom 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 hydroloom?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and hydroloom 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 hydroloom?
Top hydroloom alternatives in Analytics are ranked by recent ship velocity. Browse the "hydroloom alternatives" section above for the current picks, or visit /alternatives/hydroloom for the full list with editorial commentary on each.