gps2gtfs
gps2gtfs spent a release making its docs stop describing functions it does not have.
Comparison · Analytics
glyexp vs pedmut
A side-by-side editorial comparison of glyexp and pedmut — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r packages
glyexp vs pedmut: 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 pedmut?
pedmut turns awkward mutation models into ones the likelihood engine can actually handle.
pedmut builds and transforms the mutation models used in pedigree likelihood calculations. Its recent arc is a toolkit of model transformations: makeReversible() with three methods, makeStationary() replacing the older stabilize(), adjustRate() for tuning overall mutation rate, and lumpMutSpecial() for lumping models that strong lumpability cannot handle. The most recent release is narrow, adding a programmatic output format to getParams().
glyexp vs pedmut: 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.
pedmut
0.0ANALYTICS
pedmut turns awkward mutation models into ones the likelihood engine can actually handle.
◆ Current state
pedmut builds and transforms the mutation models used in pedigree likelihood calculations. Its recent arc is a toolkit of model transformations: makeReversible() with three methods, makeStationary() replacing the older stabilize(), adjustRate() for tuning overall mutation rate, and lumpMutSpecial() for lumping models that strong lumpability cannot handle. The most recent release is narrow, adding a programmatic output format to getParams().
◆ Where it's heading
The consistent goal is making models satisfy the mathematical properties downstream algorithms require. Reversibility, stationarity, and lumpability each unlock something in pedprobr, and the package keeps adding ways to coerce an arbitrary model into having them. lumpMutSpecial() is explicitly incomplete, described as covering only some cases with more possibly to follow, which sets up the main open thread.
◆ Prediction
Expect additional special lumping cases to be implemented, since the package documents the current coverage as partial and pedprobr's likelihood performance depends directly on it.
Alternatives to glyexp and pedmut
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 pedmut.
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.
pedbuildr
pedbuildr reconstructs pedigrees from DNA, and it just got much faster at the search.
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.
See all glyexp alternatives → · See all pedmut alternatives →
Recent activity from glyexp and pedmut
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
- 2mo agopedmutgetParams() gains a programmatic output format
- 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
- 1y agopedmutSpecial lumping arrives for un-lumpable models
- 1y agopedmutReversibility transformations and rate adjustment
- 2y agopedmutMutation rate and boundedness diagnostics
- 3y agopedmutPM stabilisation and multi-lump strong lumpability
- 3y agopedmutlumpedModel() wrapper and lumping speedups
Frequently asked questions
What is the difference between glyexp and pedmut?
Both compete on the same themes — r packages — within Analytics. glyexp and pedmut 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 pedmut?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. glyexp and pedmut 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 pedmut?
Top pedmut alternatives in Analytics are ranked by recent ship velocity. Browse the "pedmut alternatives" section above for the current picks, or visit /alternatives/pedmut for the full list with editorial commentary on each.