STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
dissmapr vs GeneNMF
A side-by-side editorial comparison of dissmapr and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
dissmapr vs GeneNMF: at a glance
What is dissmapr?
dissmapr spent its first releases becoming citable rather than adding methods.
dissmapr provides an R workflow for compositional dissimilarity and turnover — occurrence data through spatial gridding and environmental linkage to order-wise dissimilarity and bioregional mapping. All three releases to date are infrastructure: a first citable archive in June 2026, then a maturity release aligning the package with the B-Cubed software development guide. The ten-function pipeline described in the notes has not changed across them.
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.
dissmapr vs GeneNMF: editorial side-by-side
dissmapr
0.0ANALYTICS
dissmapr spent its first releases becoming citable rather than adding methods.
◆ Current state
dissmapr provides an R workflow for compositional dissimilarity and turnover — occurrence data through spatial gridding and environmental linkage to order-wise dissimilarity and bioregional mapping. All three releases to date are infrastructure: a first citable archive in June 2026, then a maturity release aligning the package with the B-Cubed software development guide. The ten-function pipeline described in the notes has not changed across them.
◆ Where it's heading
The work is compliance-shaped rather than method-shaped: explicit @importFrom in place of whole-namespace imports, library() calls removed from package code, roughly 11 MB of development caches dropped, a runnable README quick-start, and Zenodo archival with CITATION.cff and codemeta.json. dissmapr moves in lockstep with its B-Cubed sibling invasimapr — both tagged 0.1.0 within three minutes of each other and 0.2.0 on the same day — so releases here reflect project-wide standards deadlines more than package-specific work. The stated roadmap of additional ecological distance metrics has not yet landed.
◆ Prediction
With standards work now signed off and R CMD check clean, the next release is the first real chance for the roadmap items — additional ecological distance metrics — to arrive.
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 dissmapr 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 dissmapr 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 dissmapr alternatives → · See all GeneNMF alternatives →
Recent activity from dissmapr and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agodissmaprVersion bump; notes identical to 0.2.0
- 1mo agodissmaprB-Cubed standards alignment, docs overhaul and a citable DOI
- 1mo agodissmaprdissmapr v0.1.0: First citable release
- 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
Frequently asked questions
What is the difference between dissmapr and GeneNMF?
They serve adjacent needs but don't currently overlap on shipped themes. dissmapr 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 dissmapr better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. dissmapr 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 dissmapr?
Top dissmapr alternatives in Analytics are ranked by recent ship velocity. Browse the "dissmapr alternatives" section above for the current picks, or visit /alternatives/dissmapr 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.