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Comparison · Infra & APIs
PEIMAN2 vs selection.index
A side-by-side editorial comparison of PEIMAN2 and selection.index — release velocity, themes, recent moves, and the top alternatives to consider.
PEIMAN2 vs selection.index: at a glance
What is PEIMAN2?
PEIMAN2 cut its annotation database loose from its release cycle without breaking CRAN.
PEIMAN2 does enrichment analysis over post-translational modifications, testing whether a protein list is enriched for particular PTMs against UniProt-derived annotations, with translation functions bridging to mass spectrometry workflows. Its answers are only as current as its bundled database, and until June that database could only be refreshed by releasing a new package version. Version 1.1.0 changes that.
What is selection.index?
A dormant plant-breeding package returns as a genomic selection index suite
selection.index computes selection indices for plant breeding — weighting several traits into one number breeders can rank on. After two years of silence it shipped 2.0.0 in March 2026, and the package is barely recognisable: snake_case throughout, an Rcpp and RcppEigen computational core, and index families for genomic data, marker data, multi-stage trials and constrained genetic gain sitting beside the original phenotypic ones.
PEIMAN2 vs selection.index: editorial side-by-side
PEIMAN2
0.0INFRA · APIS
PEIMAN2 cut its annotation database loose from its release cycle without breaking CRAN.
◆ Current state
PEIMAN2 does enrichment analysis over post-translational modifications, testing whether a protein list is enriched for particular PTMs against UniProt-derived annotations, with translation functions bridging to mass spectrometry workflows. Its answers are only as current as its bundled database, and until June that database could only be refreshed by releasing a new package version. Version 1.1.0 changes that.
◆ Where it's heading
The package has been moving from a fixed snapshot toward versioned, user-selectable data. Earlier releases updated the bundled database in place — 1.0.0 shipped the March 2025 version and said little else — which meant the annotation vintage was whatever the package version implied. Now update_peiman_database() downloads and caches external database files and UniProt PTM lists, enrichment workflows take a database_version argument, and the mass-spec translators take a ptmlist_version, so an analysis can pin a dated database rather than a package release. The CRAN-safe default is preserved deliberately: loading, examples and checks still use the bundled internal data and need no network.
◆ Prediction
Version pinning is now expressible but the release notes do not describe how a chosen version is recorded in output, so surfacing the active database version in results is the natural companion. The database and the UniProt PTM list are versioned separately, which leaves room for a combined manifest.
selection.index
0.0INFRA · APIS
A dormant plant-breeding package returns as a genomic selection index suite
◆ Current state
selection.index computes selection indices for plant breeding — weighting several traits into one number breeders can rank on. After two years of silence it shipped 2.0.0 in March 2026, and the package is barely recognisable: snake_case throughout, an Rcpp and RcppEigen computational core, and index families for genomic data, marker data, multi-stage trials and constrained genetic gain sitting beside the original phenotypic ones.
◆ Where it's heading
The first version series added one function at a time — combinatorial indices, then genetic advance, then mean performance under randomised block designs — against a fixed phenotypic framing. Version 2.0.0 abandons that framing rather than extending it. Genomic and marker information become inputs the package understands, multi-cycle simulation becomes a built-in toolset, and the old combinatorial entry points are replaced by a named lpsi(). The 2.0.1 follow-up is entirely CI and numerical-stability work, which reads like a maintainer bracing a much larger surface.
◆ Prediction
A seventeen-runner CI matrix mirroring every CRAN check flavour, added days after 2.0.0, says the immediate concern is keeping a compiled multi-family package green rather than adding to it. Expect stabilisation releases before anything new.
Alternatives to PEIMAN2 and selection.index
Other Infra & APIs 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 PEIMAN2 or selection.index.
PINstimation
A market-microstructure toolkit that keeps adding estimators as the papers land.
nzilbb.vowels
A vowel-analysis package trimming dependencies after an email address got it archived.
emuR
The R half of the EMU speech database system, fixing what was quietly broken.
BAS
A Bayesian model-averaging package spending its 2.0 on memory, not methods.
tidyplots
tidyplots keeps rebuilding its own foundations rather than layering around them.
See all PEIMAN2 alternatives → · See all selection.index alternatives →
Recent activity from PEIMAN2 and selection.index
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 2mo agoPEIMAN2Database updates decouple from package releases ⚡
- 5mo agoselection.indexCI expanded to 17 runners after the 2.0.0 rewrite
- 5mo agoselection.indexGenomic, marker and multi-stage selection indices on an Rcpp core ⚡
- 6mo agoselection.indexUnspecified general performance improvements
- 1y agoPEIMAN2Bundled database refreshed to the March 2025 UniProt vintage
- 1y agoPEIMAN2Documentation fix for the second example dataset
- 2y agoselection.indexMean performance for randomised block designs
- 2y agoPEIMAN2Background lists for SEA and PSEA; tidyverse dependency dropped
- 3y agoselection.indexsel.index() and sel.score.rank() removed for comb.indices()
- 4y agoselection.indexGenetic advance calculation added
Frequently asked questions
What is the difference between PEIMAN2 and selection.index?
They serve adjacent needs but don't currently overlap on shipped themes. PEIMAN2 and selection.index 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 PEIMAN2 better than selection.index?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. PEIMAN2 and selection.index 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 Infra & APIs products to evaluate alongside.
What are the best alternatives to PEIMAN2?
Top PEIMAN2 alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "PEIMAN2 alternatives" section above for the current picks, or visit /alternatives/peiman2 for the full list with editorial commentary on each.
What are the best alternatives to selection.index?
Top selection.index alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "selection.index alternatives" section above for the current picks, or visit /alternatives/selection-index for the full list with editorial commentary on each.