STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs TLF-Library
A side-by-side editorial comparison of GeneNMF and TLF-Library — release velocity, themes, recent moves, and the top alternatives to consider.
GeneNMF vs TLF-Library: 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 TLF-Library?
The Open Systems Pharmacology plotting layer spent 2025 absorbing a ggplot2 major break.
tlf is the plotting library behind Open Systems Pharmacology's tables, listings and figures — a ggplot2 wrapper producing the PK/PD reporting output the OSP suite generates. Recent work splits into two strands: a feature set adding Lower Limit Of Quantification annotation to time-profile and observed-vs-predicted plots alongside a reworked axis-limits API, and then hot fixes to survive ggplot2 v4.0.0's breaking changes. The axis change is the substantive one, separating cropping the view from filtering the data behind it.
GeneNMF vs TLF-Library: 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.
TLF-Library
0.0ANALYTICS
The Open Systems Pharmacology plotting layer spent 2025 absorbing a ggplot2 major break.
◆ Current state
tlf is the plotting library behind Open Systems Pharmacology's tables, listings and figures — a ggplot2 wrapper producing the PK/PD reporting output the OSP suite generates. Recent work splits into two strands: a feature set adding Lower Limit Of Quantification annotation to time-profile and observed-vs-predicted plots alongside a reworked axis-limits API, and then hot fixes to survive ggplot2 v4.0.0's breaking changes. The axis change is the substantive one, separating cropping the view from filtering the data behind it.
◆ Where it's heading
The library is maturing into a stable reporting dependency rather than growing new plot types — the newest releases are watermark placement, log-tick safety and upstream compatibility, not new figures. Its exposure is to ggplot2: v4.0.0 required same-day hot fixes, which is the risk profile of a wrapper this thin. Note that this feed's version numbers and publication stamps disagree, with 1.5.170 stamped four months before the lower-numbered 1.5.158, so the release order has to be read from version numbers and the changelog ranges rather than from the feed order.
◆ Prediction
With the ggplot2 v4 fallout patched and the LLOQ work promoted to a stable 1.6 line, the next releases most likely continue as small rendering fixes. Nothing in these entries points to a new plot class in progress.
Alternatives to GeneNMF and TLF-Library
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 TLF-Library.
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 TLF-Library alternatives →
Recent activity from GeneNMF and TLF-Library
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 9mo agoTLF-LibraryWatermark positioning decoupled from plot scales
- 11mo agoTLF-LibraryHot fixes for ggplot2 v4.0.0 breaking changes
- 11mo agoTLF-LibraryLLOQ annotation and axis cropping split from data filtering
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agoTLF-LibraryDev build introducing LLOQ plots and the xAxisLimits rename
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agoTLF-LibraryError-bar cap fixes atop a restated feature list
- 1y agoGeneNMFSimilarity heatmap downsampling and meta-program removal
- 1y agoTLF-LibraryDual-axis plots stop tripping cowplot
- 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 GeneNMF and TLF-Library?
They serve adjacent needs but don't currently overlap on shipped themes. GeneNMF and TLF-Library 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 TLF-Library?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and TLF-Library 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 TLF-Library?
Top TLF-Library alternatives in Analytics are ranked by recent ship velocity. Browse the "TLF-Library alternatives" section above for the current picks, or visit /alternatives/tlf-library for the full list with editorial commentary on each.