gps2gtfs
gps2gtfs spent a release making its docs stop describing functions it does not have.
Comparison · Analytics
glyexp vs pedbuildr
A side-by-side editorial comparison of glyexp and pedbuildr — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r packages
glyexp vs pedbuildr: at a glance
What is glyexp?
glyexp is retiring its own data container and handing the job to Bioconductor.
glyexp is the container layer under the glycoverse stack, and it just changed what that container is. Versions 0.15.0 and 0.16.0 introduced GlycomicSE and GlycoproteomicSE as SummarizedExperiment subclasses, taught the dplyr-style verbs to operate on them, and then deprecated the legacy experiment() constructor and its accessors. Earlier releases in the window were narrower: as_pseudo_glycome(), a magrittr-free rewrite, and an offline standardize_variable().
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.
glyexp vs pedbuildr: editorial side-by-side
glyexp
0.0ANALYTICS
glyexp is retiring its own data container and handing the job to Bioconductor.
◆ Current state
glyexp is the container layer under the glycoverse stack, and it just changed what that container is. Versions 0.15.0 and 0.16.0 introduced GlycomicSE and GlycoproteomicSE as SummarizedExperiment subclasses, taught the dplyr-style verbs to operate on them, and then deprecated the legacy experiment() constructor and its accessors. Earlier releases in the window were narrower: as_pseudo_glycome(), a magrittr-free rewrite, and an offline standardize_variable().
◆ Where it's heading
The package is moving from a bespoke object model to the Bioconductor one, and doing it in explicitly numbered stages tracked in a single issue (glyexp#15). Stage I added the subclasses as experimental; Stage II deprecated the old container and pushed the migration through ten sibling packages within days. The tidy manipulation verbs are being kept as the compatibility bridge, which suggests the dplyr surface is what the maintainer considers glyexp's actual contribution once the container is someone else's.
◆ Prediction
Expect a Stage III release that removes the deprecated experiment() constructor and accessors outright, leaving GlycomicSE and GlycoproteomicSE as the only supported containers.
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 glyexp 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 glyexp 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 glyexp alternatives → · See all pedbuildr alternatives →
Recent activity from glyexp and pedbuildr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agoglyexpglyexp deprecates its own container for SummarizedExperiment ⚡
- 1mo agoglyexpExperimental GlycomicSE and GlycoproteomicSE containers land
- 1mo agoglyexpfrom_se() metadata fixes and dataset refresh
- 1mo agopedbuildrmirai parallelism and faster pedigree enumeration
- 4mo agoglyexpfilter_obs() and filter_var() drop unused factor levels
- 4mo agoglyexpas_pseudo_glycome() converts glycoproteomics to glycomics
- 5mo agoglyexpstandardize_variable() drops its UniProt network dependency
- 2y agopedbuildrpedCollection class and an inbreeding ceiling
Frequently asked questions
What is the difference between glyexp and pedbuildr?
Both compete on the same themes — r packages — within Analytics. glyexp 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 glyexp better than pedbuildr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. glyexp 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 glyexp?
Top glyexp alternatives in Analytics are ranked by recent ship velocity. Browse the "glyexp alternatives" section above for the current picks, or visit /alternatives/glyexp 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.