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Comparison · Analytics
glystats vs pedbuildr
A side-by-side editorial comparison of glystats and pedbuildr — release velocity, themes, recent moves, and the top alternatives to consider.
glystats vs pedbuildr: at a glance
What is glystats?
glystats keeps deleting analyses it decided belong somewhere else.
glystats provides the statistical tests behind glycoverse: differential analysis, clustering, dimensionality reduction, and until recently enrichment. The last four releases are mostly subtraction. WGCNA and consensus clustering were removed in 0.10.0 as too interactive for a pipeline package, the enrichment functions were deprecated in the same release and deleted in 0.11.0 in favor of glyfun, and 0.11.0 also removed every gly_*_() matrix and vector interface. What remains accepts SummarizedExperiment inputs.
What is pedbuildr?
pedbuildr reconstructs pedigrees from DNA, and it just got much faster at the search.
pedbuildr infers pedigree structure from marker data by scoring candidate pedigrees against likelihoods. Version 0.4.0 moved reconstruct() to mirai for parallel likelihood computation, deprecated the old numCores argument, and picked up the improved loop breaking from pedtools and pedprobr, which lets many complex looped pedigrees succeed where they previously failed. buildPeds() also got significantly faster in its default configuration where mating between lineally related individuals is disallowed.
glystats vs pedbuildr: editorial side-by-side
glystats
0.0ANALYTICS
glystats keeps deleting analyses it decided belong somewhere else.
◆ Current state
glystats provides the statistical tests behind glycoverse: differential analysis, clustering, dimensionality reduction, and until recently enrichment. The last four releases are mostly subtraction. WGCNA and consensus clustering were removed in 0.10.0 as too interactive for a pipeline package, the enrichment functions were deprecated in the same release and deleted in 0.11.0 in favor of glyfun, and 0.11.0 also removed every gly_*_() matrix and vector interface. What remains accepts SummarizedExperiment inputs.
◆ Where it's heading
The package is narrowing on purpose. The through-line across removals is a refusal to support two calling conventions or two homes for the same analysis: containers only, no bare matrices; one enrichment implementation, in glyfun. The additive work in the window went to statistical rigor rather than surface area, with effect sizes added to the four main tests, sign bugs fixed, and the log2 pseudo-count reduced.
◆ Prediction
With the interface pruning finished, the next releases are more likely to deepen the tests that remain than to add new analysis families.
pedbuildr
0.0ANALYTICS
pedbuildr reconstructs pedigrees from DNA, and it just got much faster at the search.
◆ Current state
pedbuildr infers pedigree structure from marker data by scoring candidate pedigrees against likelihoods. Version 0.4.0 moved reconstruct() to mirai for parallel likelihood computation, deprecated the old numCores argument, and picked up the improved loop breaking from pedtools and pedprobr, which lets many complex looped pedigrees succeed where they previously failed. buildPeds() also got significantly faster in its default configuration where mating between lineally related individuals is disallowed.
◆ Where it's heading
The package is bounded by two costs: how many candidate pedigrees it enumerates and how expensive each likelihood is. The recent release attacks both, parallelizing the likelihoods and speeding up enumeration in the common case. The earlier 0.3.0 release worked on the other end, adding inbreeding limits and a proper result class so the output of a large search is manageable. Releases are infrequent, roughly three years apart in this window.
◆ Prediction
Expect the candidate generation side to receive the same attention the likelihood side just did, since search space size is the remaining bound on what pedbuildr can reconstruct.
Alternatives to glystats and pedbuildr
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 glystats or pedbuildr.
spsurvey
spsurvey has spent four years consolidating after its 5.0.0 rewrite rather than adding to it
StreamCatTools
StreamCatTools is quietly moving off web services and onto cloud-native GeoParquet
reproducible
reproducible added a windowed read path so remote GeoTiffs never fully download
qcTAF
qcTAF is building an automated checklist for reproducible fisheries assessments, one criterion at a time
rpymat
After three dormant years, rpymat returned to fix the OpenMP crash that breaks R and conda together
See all glystats alternatives → · See all pedbuildr alternatives →
Recent activity from glystats and pedbuildr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agoglystatsDocs recommend the new SE containers
- 1mo agoglystatsTests recognize both container types consistently
- 1mo agoglystatsMatrix interfaces and enrichment functions removed
- 1mo agopedbuildrmirai parallelism and faster pedigree enumeration
- 2mo agoglystatsSmaller log2 pseudo-count across DEA and clustering
- 3mo agoglystatsWGCNA and clustering dropped, enrichment deprecated
- 4mo agoglystatsEffect sizes added and test statistic signs fixed
- 2y agopedbuildrpedCollection class and an inbreeding ceiling
Frequently asked questions
What is the difference between glystats and pedbuildr?
They serve adjacent needs but don't currently overlap on shipped themes. glystats and pedbuildr 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 glystats better than pedbuildr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. glystats and pedbuildr 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 glystats?
Top glystats alternatives in Analytics are ranked by recent ship velocity. Browse the "glystats alternatives" section above for the current picks, or visit /alternatives/glystats for the full list with editorial commentary on each.
What are the best alternatives to pedbuildr?
Top pedbuildr alternatives in Analytics are ranked by recent ship velocity. Browse the "pedbuildr alternatives" section above for the current picks, or visit /alternatives/pedbuildr for the full list with editorial commentary on each.