midr
A black-box interpreter reaches CRAN, then learns multi-class and survival responses
Comparison · Infra & APIs
PEIMAN2 vs rstudio.prefs
A side-by-side editorial comparison of PEIMAN2 and rstudio.prefs — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-packages
PEIMAN2 vs rstudio.prefs: 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 rstudio.prefs?
Four years dormant, rstudio.prefs returns under a new maintainer.
The package scripts RStudio's own settings — preferences, secondary repositories, keyboard shortcuts — as code you can drop into a project or an onboarding doc. After 0.1.9 in July 2022 it went quiet for four years. 0.2.0 ends that with a maintainer handoff from Daniel D. Sjoberg to S.A. van der Wulp, a shortcut-removal path, and a fix for a corrupted addins.json entry that made reassigned shortcuts fail silently.
PEIMAN2 vs rstudio.prefs: 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.
rstudio.prefs
2.5INFRA · APIS
Four years dormant, rstudio.prefs returns under a new maintainer.
◆ Current state
The package scripts RStudio's own settings — preferences, secondary repositories, keyboard shortcuts — as code you can drop into a project or an onboarding doc. After 0.1.9 in July 2022 it went quiet for four years. 0.2.0 ends that with a maintainer handoff from Daniel D. Sjoberg to S.A. van der Wulp, a shortcut-removal path, and a fix for a corrupted addins.json entry that made reassigned shortcuts fail silently.
◆ Where it's heading
The through-line is teaching every setter how to unset. Secondary repositories got NULL removal back in 0.1.6; 0.2.0 extends the same convention to keyboard shortcuts. Most of the rest of 0.2.0 is arrears — a stale documentation URL that hid preferences such as enable_splash_screen, a deprecated purrr::update_list() call, and check_shortcut_consistency() erroring early on an unknown name.
◆ Prediction
With a new maintainer and refreshed GitHub Actions, the near-term work is likely more catch-up of the same kind: remaining deprecated dependencies and the preference list that fetch_rstudio_prefs() reads from RStudio's docs. Nothing in these notes points past RStudio settings as the scope.
Alternatives to PEIMAN2 and rstudio.prefs
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 rstudio.prefs.
GeoThinneR
Spatial thinning grows a result object, and the API breaks to make room for it
selection.index
A dormant plant-breeding package returns as a genomic selection index suite
packageRank
CRAN download analytics maintained one micro-change at a time, hundreds per year
melodi
INSEE's statistics API gets a French R client that keeps meeting its edge cases
bulkreadr
A bulk file reader became a labelled-survey-data toolkit, then went quiet
See all PEIMAN2 alternatives → · See all rstudio.prefs alternatives →
Recent activity from PEIMAN2 and rstudio.prefs
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 8h agorstudio.prefsShortcut removal, an addins.json fix, and a new maintainer
- 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
- 4y agorstudio.prefsPreferences now read and written through rstudioapi
- 4y agorstudio.prefsConfig files left alone when nothing would change
- 4y agorstudio.prefsSecondary repositories can be deleted again
- 4y agorstudio.prefsRepository removal via NULL; config path helpers exported
- 5y agorstudio.prefsDocumentation, error messages, and array-type caution
Frequently asked questions
What is the difference between PEIMAN2 and rstudio.prefs?
Both compete on the same themes — r-packages — within Infra & APIs. rstudio.prefs is currently shipping more aggressively (velocity 2.5 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 rstudio.prefs?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. rstudio.prefs is currently shipping more aggressively (velocity 2.5 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 rstudio.prefs?
Top rstudio.prefs alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "rstudio.prefs alternatives" section above for the current picks, or visit /alternatives/rstudio-prefs for the full list with editorial commentary on each.