ggpointless
ggpointless keeps adding the ggplot2 layers nobody else bothered to write.
Comparison · Infra & APIs
PEIMAN2 vs Skipper
A side-by-side editorial comparison of PEIMAN2 and Skipper — release velocity, themes, recent moves, and the top alternatives to consider.
PEIMAN2 vs Skipper: 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 Skipper?
Skipper trims a 4x memory regression out of routesrv, days after shipping h2c
Zalando's HTTP router ships patch tags almost daily, and most carry a single dependency bump or a one-line auth fix. The substance in this window is v0.27.63, which stops routesrv holding an uncompressed route tree alongside the compressed buffer: retained memory in the release's own benchmark falls from 30.7 MB to 2.0 MB, undoing most of the 4x increase zone-aware routing had introduced. Around it sit narrow auth repairs, and an eskip parser change that finally accepts negative numeric arguments in predicates and filters.
PEIMAN2 vs Skipper: 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.
Skipper
5.0INFRA · APIS
Skipper trims a 4x memory regression out of routesrv, days after shipping h2c
◆ Current state
Zalando's HTTP router ships patch tags almost daily, and most carry a single dependency bump or a one-line auth fix. The substance in this window is v0.27.63, which stops routesrv holding an uncompressed route tree alongside the compressed buffer: retained memory in the release's own benchmark falls from 30.7 MB to 2.0 MB, undoing most of the 4x increase zone-aware routing had introduced. Around it sit narrow auth repairs, and an eskip parser change that finally accepts negative numeric arguments in predicates and filters.
◆ Where it's heading
Two threads run through the recent tags. The data path keeps getting real work - leastRequests balancing, then h2c end to end in v0.27.57, now the memory cost of zone-aware routing being paid back. The auth filters, by contrast, are only being maintained: token introspection, grant auth, and now the OIDC Referer handling are fixes rather than new capability, and several are follow-ups to each other rather than independent bugs.
◆ Prediction
Zone-aware routing looks like the source of the recent memory attention, so expect further tuning around route storage and the hash computation done on every pull, which the release's second benchmark already isolates. The OIDC cookie change is the second link in an auth chain that started with the grant-auth fix, and is likely to draw another follow-up.
Alternatives to PEIMAN2 and Skipper
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 Skipper.
mpactr
mpactr spent two spring releases normalizing case in metadata after users kept tripping on it.
surveytidy
surveytidy taught every dplyr verb to operate on a whole collection of surveys at once.
surveycore
surveycore declared its API stable with every survey design type covered.
prospectr
prospectr spent its biggest release in years fixing spectra it had been quietly mangling.
standardlastprofile
A German electricity load-profile package added gas and doubled the market it serves.
See all PEIMAN2 alternatives → · See all Skipper alternatives →
Recent activity from PEIMAN2 and Skipper
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 23h agoSkipperMove OIDC flow protection from Referer to cookies
- 23h agoSkipperv0.27.63: Store routes compressed-only, decompress on demand (#4198)
- 1d agoSkipperEskip predicates and filters accept negative numbers
- 1d agoSkipperFix token introspection handling
- 1d agoSkipperFix grant auth flow
- 2d agoSkipperUpdate outdated golang.org/x dependencies
- 2mo agoPEIMAN2Database updates decouple from package releases ⚡
- 1y agoPEIMAN2Bundled database refreshed to the March 2025 UniProt vintage
- 1y agoPEIMAN2Documentation fix for the second example dataset
- 2y agoPEIMAN2Background lists for SEA and PSEA; tidyverse dependency dropped
Frequently asked questions
What is the difference between PEIMAN2 and Skipper?
They serve adjacent needs but don't currently overlap on shipped themes. Skipper is currently shipping more aggressively (velocity 5.0 vs 0.0), with 0 editorial sparks in the last 30 days against 0. See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is PEIMAN2 better than Skipper?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. Skipper is currently shipping more aggressively (velocity 5.0 vs 0.0), with 0 editorial sparks in the last 30 days against 0. 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 Skipper?
Top Skipper alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "Skipper alternatives" section above for the current picks, or visit /alternatives/skipper for the full list with editorial commentary on each.