ggtrace
A debugger for ggplot2's internals, hardening its grip as the internals it traces keep moving.
Comparison · Analytics
crossmap vs GeneNMF
A side-by-side editorial comparison of crossmap and GeneNMF — release velocity, themes, recent moves, and the top alternatives to consider.
crossmap vs GeneNMF: at a glance
What is crossmap?
crossmap's roadmap is set by purrr and furrr — it deprecates what upstream deprecates.
A small package for mapping over combinations of arguments, following purrr and furrr conventions. Its own functional additions stopped after xpluck() in 2023 and the cross_fit() clustering work in 2022. Everything since tracks upstream: xmap_raw() and future_xmap_raw() are now defunct because purrr removed map_raw() and furrr removed future_pmap_raw(), and re-exported parallel helpers now come from parallelly rather than future.
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.
crossmap vs GeneNMF: editorial side-by-side
crossmap
0.0ANALYTICS
crossmap's roadmap is set by purrr and furrr — it deprecates what upstream deprecates.
◆ Current state
A small package for mapping over combinations of arguments, following purrr and furrr conventions. Its own functional additions stopped after xpluck() in 2023 and the cross_fit() clustering work in 2022. Everything since tracks upstream: xmap_raw() and future_xmap_raw() are now defunct because purrr removed map_raw() and furrr removed future_pmap_raw(), and re-exported parallel helpers now come from parallelly rather than future.
◆ Where it's heading
The package has settled into being a compatible extension rather than an independent one — its release notes read as a mirror of purrr's and furrr's deprecation schedules. Note that the release stamps are unreliable here: several versions were backfilled minutes apart and the 0.3.x tags carry timestamps in reverse version order, so feed position says nothing about what shipped when.
◆ Prediction
Expect the next release to be driven by another purrr or furrr change rather than new functionality, since that has been the sole trigger for the last four.
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 crossmap 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 crossmap or GeneNMF.
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.
eiaapi
A thin EIA energy-data client whose whole story is making bulk queries survive the API's limits.
See all crossmap alternatives → · See all GeneNMF alternatives →
Recent activity from crossmap and GeneNMF
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 6mo agocrossmapRaw-vector mapping functions removed
- 6mo agocrossmapRe-exports moved to the parallelly namespace
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 11mo agocrossmapFuture-backed tests skipped on CRAN
- 11mo agocrossmapInternal test fixes
- 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 agocrossmapxpluck adds multi-index plucking
- 4y agocrossmapCluster specifications supported in cross_fit
Frequently asked questions
What is the difference between crossmap and GeneNMF?
They serve adjacent needs but don't currently overlap on shipped themes. crossmap 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 crossmap better than GeneNMF?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. crossmap 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 crossmap?
Top crossmap alternatives in Analytics are ranked by recent ship velocity. Browse the "crossmap alternatives" section above for the current picks, or visit /alternatives/crossmap 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.