STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
delaporte vs GeneNMF
A side-by-side editorial comparison of delaporte and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
delaporte vs GeneNMF: at a glance
What is delaporte?
A Fortran-backed Delaporte distribution package where every release is compiler and CRAN weather.
Delaporte supplies the density, distribution, quantile and random-generation functions for the Delaporte distribution — a Poisson-negative-binomial convolution used for overdispersed count data — implemented in Fortran and called through C. The only user-facing addition in the visible history is explicit OpenMP thread control via getDelapThreads() and setDelapThreads() at 8.2.0.
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.
delaporte vs GeneNMF: editorial side-by-side
delaporte
0.0ANALYTICS
A Fortran-backed Delaporte distribution package where every release is compiler and CRAN weather.
◆ Current state
Delaporte supplies the density, distribution, quantile and random-generation functions for the Delaporte distribution — a Poisson-negative-binomial convolution used for overdispersed count data — implemented in Fortran and called through C. The only user-facing addition in the visible history is explicit OpenMP thread control via getDelapThreads() and setDelapThreads() at 8.2.0.
◆ Where it's heading
The maintenance burden here is portability, not statistics. Recent entries track a Fortran suffix change for Intel compiler compatibility, architecture-specific test tolerances, type-safety corrections on values crossing the C-to-Fortran boundary, and a thread-count variable relocated from R options to an environment variable to follow an upstream R commit. The distribution functions themselves are settled; what changes is how the compiled code is built and checked across CRAN's platform matrix.
◆ Prediction
Expect the next release to follow another CRAN toolchain or Writing R Extensions policy change, as the last several have. Two of the four visible entries carry no notes at all, so this feed will keep understating what actually shipped.
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 delaporte 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 delaporte 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 delaporte alternatives → · See all GeneNMF alternatives →
Recent activity from delaporte and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agodelaporteThread limit moves to an environment variable; Fortran type checks tightened
- 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
- 3y agodelaporteExplicit OpenMP thread control functions added
- 3y agodelaporteCRAN release 8.1.1
- 3y agodelaporteCRAN release 8.1.0
Frequently asked questions
What is the difference between delaporte and GeneNMF?
Both compete on the same themes — r-package — within Analytics. delaporte 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 delaporte better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. delaporte 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 delaporte?
Top delaporte alternatives in Analytics are ranked by recent ship velocity. Browse the "delaporte alternatives" section above for the current picks, or visit /alternatives/delaporte 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.