gps2gtfs
gps2gtfs spent a release making its docs stop describing functions it does not have.
Comparison · Analytics
glyanno vs pedtools
A side-by-side editorial comparison of glyanno and pedtools — release velocity, themes, recent moves, and the top alternatives to consider.
glyanno vs pedtools: at a glance
What is glyanno?
Glycan annotation stops depending on the database having seen the structure before.
glyanno resolves mass spectrometry observations into glycan compositions and structures, converting between m/z, composition and structure, filling in missing detail on partial structures, and mapping results to GlyTouCan accessions. The newest release adds de novo reconstruction of topological N-glycans, falling back to the topological database only when reconstruction is not possible. Batch performance was reworked at the same time, with vector inputs reusing prepared databases and direct lookups instead of repeating setup per element.
What is pedtools?
pedtools rewrote loop breaking and made a class of pedigrees analyzable for the first time.
pedtools is the foundation of the ped suite, holding the pedigree data structures every other package builds on. Version 2.11.0 revamped the loop breaking algorithm so founders can serve as loop breakers and one individual can break several loops, which makes likelihood calculations possible in pedigrees that previously could not be handled at all. Loop detection also became mandatory and faster, and the surrounding releases have steadily added query and construction helpers.
glyanno vs pedtools: editorial side-by-side
glyanno
3.8ANALYTICS
Glycan annotation stops depending on the database having seen the structure before.
◆ Current state
glyanno resolves mass spectrometry observations into glycan compositions and structures, converting between m/z, composition and structure, filling in missing detail on partial structures, and mapping results to GlyTouCan accessions. The newest release adds de novo reconstruction of topological N-glycans, falling back to the topological database only when reconstruction is not possible. Batch performance was reworked at the same time, with vector inputs reusing prepared databases and direct lookups instead of repeating setup per element.
◆ Where it's heading
The consistent theme is making ambiguous results honest and predictable. return_best moved from returning a shortened tibble to a vector aligned with the input, with NA for unmatched glycans; matching concrete compositions against a generic database now errors instead of silently returning nothing; zero-length database arguments are rejected. Alongside that, functions belonging elsewhere have been pushed down into glyrepr rather than duplicated, which is the same boundary discipline visible across this cohort. Version churn is largely driven by upstream: two of the last six entries exist to absorb breaking changes in glyrepr.
◆ Prediction
De novo reconstruction currently covers topological N-glycans only, so extending it to other structure levels or to O-glycans is the natural next step. The performance work suggests batch annotation of full experiments is now the primary use being optimised for.
pedtools
0.0ANALYTICS
pedtools rewrote loop breaking and made a class of pedigrees analyzable for the first time.
◆ Current state
pedtools is the foundation of the ped suite, holding the pedigree data structures every other package builds on. Version 2.11.0 revamped the loop breaking algorithm so founders can serve as loop breakers and one individual can break several loops, which makes likelihood calculations possible in pedigrees that previously could not be handled at all. Loop detection also became mandatory and faster, and the surrounding releases have steadily added query and construction helpers.
◆ Where it's heading
The package has been working toward this for over a year. Version 2.8.0 replaced the igraph-based loop breaker with a custom implementation, 2.8.1 made findLoopBreakers() substantially faster in large pedigrees, and 2.11.0 rewrote the algorithm outright. The new methods ship disabled by default while downstream packages catch up, which is a deliberately staged rollout rather than a flag day. Alongside that, the additive work is small, well-scoped helpers: children2(), addSibling(), isHomozygous(), trim(), nChildren().
◆ Prediction
Expect the new loop breaking methods to become the default once pedprobr, forrel, and dvir have all shipped support for them, since the only stated reason for the opt-in flag is downstream readiness.
Alternatives to glyanno and pedtools
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 glyanno or pedtools.
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 glyanno alternatives → · See all pedtools alternatives →
Recent activity from glyanno and pedtools
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 24d agoglyannoDe novo reconstruction of topological N-glycans, with database fallback ⚡
- 1mo agopedtoolsLoop breaking rewrite makes intractable pedigrees analyzable ⚡
- 3mo agoglyannoGlyTouCan accession mapping and anomeric position filling
- 3mo agoglyannoFixes an enhance_struc() break from glyrepr 0.11.0
- 4mo agoglyannoExplicit empty return from com_to_struc()
- 4mo agoglyannoreturn_best output aligns with input length; silent empty matches now error
- 5mo agoglyannoto_level parameter removed from enhance_struc()
- 6mo agopedtoolsGenotype comparison helpers and more flexible subsetting
- 9mo agopedtoolsmergePed() handles marker data; genotype removal simplified
- 1y agopedtoolssetSNPs() accepts genotypes; proband arrows in plots
- 1y agopedtoolstrim() prunes uninformative leaves; loop breaker search sped up
- 1y agopedtoolsigraph dependency dropped for a custom loop breaker
Frequently asked questions
What is the difference between glyanno and pedtools?
They serve adjacent needs but don't currently overlap on shipped themes. glyanno is currently shipping more aggressively (velocity 3.8 vs 0.0), with 1 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 glyanno better than pedtools?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. glyanno is currently shipping more aggressively (velocity 3.8 vs 0.0), with 1 editorial sparks in the last 30 days against 0. For your specific use case, the alternatives sections above list other Analytics products to evaluate alongside.
What are the best alternatives to glyanno?
Top glyanno alternatives in Analytics are ranked by recent ship velocity. Browse the "glyanno alternatives" section above for the current picks, or visit /alternatives/glyanno for the full list with editorial commentary on each.
What are the best alternatives to pedtools?
Top pedtools alternatives in Analytics are ranked by recent ship velocity. Browse the "pedtools alternatives" section above for the current picks, or visit /alternatives/pedtools for the full list with editorial commentary on each.