STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs questionr
A side-by-side editorial comparison of GeneNMF and questionr — release velocity, themes, recent moves, and the top alternatives to consider.
GeneNMF vs questionr: 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 questionr?
questionr's survey helpers are finished; recent releases only keep pace with R-devel.
A long-running toolkit for survey data in R — proportion tables, weighted counts, and the interactive irec(), iorder() and icut() addins for recoding. The last functional release was 0.8.0 in March 2025: a new freqtable() function, prop(), cprop() and rprop() extended to tables of three or more dimensions, and the addins moved onto the native pipe and forcats' current API. Both releases since exist purely to fix tests broken by R-devel changes to table internals.
GeneNMF vs questionr: 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.
questionr
0.0ANALYTICS
questionr's survey helpers are finished; recent releases only keep pace with R-devel.
◆ Current state
A long-running toolkit for survey data in R — proportion tables, weighted counts, and the interactive irec(), iorder() and icut() addins for recoding. The last functional release was 0.8.0 in March 2025: a new freqtable() function, prop(), cprop() and rprop() extended to tables of three or more dimensions, and the addins moved onto the native pipe and forcats' current API. Both releases since exist purely to fix tests broken by R-devel changes to table internals.
◆ Where it's heading
This is a stable package in compatibility-maintenance mode, where the release trigger is upstream churn rather than user demand. The functional work that does appear follows a consistent line — generalising the table functions beyond two dimensions, and keeping the interactive recoding addins aligned with current tidyverse idioms rather than the deprecated ones they were written against. The same maintainer's rainette shipped its own upstream-compatibility fix in the same window.
◆ Prediction
Expect the next release to be another R-devel or tidyverse compatibility fix; nothing in the entries points to new functionality.
Alternatives to GeneNMF and questionr
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 questionr.
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 questionr alternatives →
Recent activity from GeneNMF and questionr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 6mo agoquestionrR-devel test fix for NA naming in tables
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agoquestionrR-devel test fix for table subset classes
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agoquestionrfreqtable added; proportion tables handle three or more dimensions
- 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 agoquestionrAddins handle non-syntactic variable names
- 4y agoquestionrforcats errors on numeric variables fixed
- 4y agoquestionricut default changed; rp2018 dataset replaces rp99
Frequently asked questions
What is the difference between GeneNMF and questionr?
They serve adjacent needs but don't currently overlap on shipped themes. GeneNMF and questionr 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 questionr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and questionr 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 questionr?
Top questionr alternatives in Analytics are ranked by recent ship velocity. Browse the "questionr alternatives" section above for the current picks, or visit /alternatives/questionr for the full list with editorial commentary on each.