gps2gtfs
gps2gtfs spent a release making its docs stop describing functions it does not have.
Comparison · Analytics
glyvis vs pedbuildr
A side-by-side editorial comparison of glyvis and pedbuildr — release velocity, themes, recent moves, and the top alternatives to consider.
glyvis vs pedbuildr: at a glance
What is glyvis?
glyvis keeps losing plot functions as the packages behind them get reorganized.
glyvis is the plotting layer for glycoverse results. Its recent releases are dominated by two forces it does not control: glyexp's container migration, which it absorbed in 0.7.0 by accepting SummarizedExperiment inputs, and glystats' function removals, which cost it first the WGCNA and consensus-clustering autoplot methods and then the entire enrichment plotting surface. Its own additions in the window are narrow, mostly label handling and NA robustness.
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.
glyvis vs pedbuildr: editorial side-by-side
glyvis
0.0ANALYTICS
glyvis keeps losing plot functions as the packages behind them get reorganized.
◆ Current state
glyvis is the plotting layer for glycoverse results. Its recent releases are dominated by two forces it does not control: glyexp's container migration, which it absorbed in 0.7.0 by accepting SummarizedExperiment inputs, and glystats' function removals, which cost it first the WGCNA and consensus-clustering autoplot methods and then the entire enrichment plotting surface. Its own additions in the window are narrow, mostly label handling and NA robustness.
◆ Where it's heading
The package is being pruned from upstream rather than expanded from within. Every breaking change in the last four releases is a removal triggered by a sibling package dropping the function that produced the object being plotted. With enrichment now living in glyfun, the plotting for it has to be rebuilt somewhere, and glyvis is the obvious home.
◆ Prediction
Expect enrichment plotting to return once glyfun's result objects stabilize, since the visualizations were removed for want of an upstream producer rather than because users stopped needing them.
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 glyvis 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 glyvis or pedbuildr.
ducksemantics
ducksemantics puts an ontology graph and ColBERT retrieval inside DuckDB, callable from R.
dvir
dvir keeps making disaster victim identification a single call instead of a workflow.
forrel
forrel is getting faster at the simulations forensic kinship work actually spends its time on.
pedFamilias
pedFamilias exists to read one legacy file format, and it has that job nearly finished.
pedmut
pedmut turns awkward mutation models into ones the likelihood engine can actually handle.
See all glyvis alternatives → · See all pedbuildr alternatives →
Recent activity from glyvis and pedbuildr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agoglyvisDocs recommend the new SE containers
- 1mo agoglyvisplot_logo() detects glycoproteomics across both containers
- 1mo agoglyvisPlots accept SummarizedExperiment; enrichment plots removed
- 1mo agopedbuildrmirai parallelism and faster pedigree enumeration
- 3mo agoglyvisStale WGCNA and clustering autoplot methods removed
- 6mo agoglyvisDependencies move to the r-universe repository
- 7mo agoglyvisplot_logo() fetches UniProt sequences automatically
- 2y agopedbuildrpedCollection class and an inbreeding ceiling
Frequently asked questions
What is the difference between glyvis and pedbuildr?
They serve adjacent needs but don't currently overlap on shipped themes. glyvis 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 glyvis better than pedbuildr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. glyvis 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 glyvis?
Top glyvis alternatives in Analytics are ranked by recent ship velocity. Browse the "glyvis alternatives" section above for the current picks, or visit /alternatives/glyvis 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.