qqman
The Manhattan-plot package for GWAS results, finished and dormant since 2017.
Comparison · Analytics
gtfstools vs gwasvcf
A side-by-side editorial comparison of gtfstools and gwasvcf — release velocity, themes, recent moves, and the top alternatives to consider.
gtfstools vs gwasvcf: at a glance
What is gtfstools?
gtfstools stopped guarding its own object model and started accepting everyone else's.
gtfstools reads, edits, filters and validates GTFS public transport feeds in R on a data.table backend. Since 1.3.0 it accepts GTFS objects produced by other packages such as gtfsio and tidytransit, converting them through an as_dt_gtfs() generic. Validation runs MobilityData's canonical validator, now supported through v6.0.0.
What is gwasvcf?
gwasvcf has stopped adding features and now just keeps proxy matching from failing.
gwasvcf reads and queries GWAS summary statistics stored as VCF, with LD proxy lookup as its most-used entry point. Every release in the visible window is a fix, and all but one land in or around proxy_match(). The last functional addition was gwasvcf_to_summaryset() in 0.1.2, which hands data to gwasglue2 rather than doing new work here.
gtfstools vs gwasvcf: editorial side-by-side
gtfstools
0.0ANALYTICS
gtfstools stopped guarding its own object model and started accepting everyone else's.
◆ Current state
gtfstools reads, edits, filters and validates GTFS public transport feeds in R on a data.table backend. Since 1.3.0 it accepts GTFS objects produced by other packages such as gtfsio and tidytransit, converting them through an as_dt_gtfs() generic. Validation runs MobilityData's canonical validator, now supported through v6.0.0.
◆ Where it's heading
The package built out a wide function surface first — filters, geometry conversion, speed and duration calculations — then turned outward. Delegating validation to MobilityData's validator and accepting other packages' objects both trade self-sufficiency for a position inside the wider GTFS ecosystem. Deprecations are handled slowly, with old behaviour left as the default for a release or more.
◆ Prediction
Expect continued validator version tracking and further completion of the deprecation cycle around filter_by_stop_id()'s full_trips behaviour.
gwasvcf
0.0ANALYTICS
gwasvcf has stopped adding features and now just keeps proxy matching from failing.
◆ Current state
gwasvcf reads and queries GWAS summary statistics stored as VCF, with LD proxy lookup as its most-used entry point. Every release in the visible window is a fix, and all but one land in or around proxy_match(). The last functional addition was gwasvcf_to_summaryset() in 0.1.2, which hands data to gwasglue2 rather than doing new work here.
◆ Where it's heading
The package is in custodial maintenance inside the MRC IEU OpenGWAS stack, and its releases are reactive: each one answers a specific user-reported failure, credited to the reporter. The 0.1.6 pattern is telling — rather than replace the proxy VCF construction, it keeps the original path and adds a fallback only for inputs that fail, so existing results are left bit-for-bit unchanged.
◆ Prediction
Expect further narrow robustness fixes to proxy_match() driven by user-reported VCF shapes; nothing in the entries suggests new analysis capability is being built here rather than in gwasglue2.
Alternatives to gtfstools and gwasvcf
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 gtfstools or gwasvcf.
constants
The R package for CODATA constants rebuilt its symbol table on NIST's naming so future updates stop being hand work.
austraits
The R client for AusTraits spends its releases chasing the dataset it reads.
ggdemetra
A ggplot2 layer for seasonal adjustment output, filling in one plot type at a time.
fossilsim
A fossil-record simulator that quietly grew a trait-evolution engine.
tern.rbmi
Reference-based multiple imputation tables, shipping only what CRAN checks demand.
See all gtfstools alternatives → · See all gwasvcf alternatives →
Recent activity from gtfstools and gwasvcf
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 5mo agogwasvcfproxy_match() gains a fallback VCF construction path
- 8mo agogwasvcfproxy_match() handles multi-sample VCFs
- 1y agogwasvcfsqlite3 declared in SystemRequirements
- 1y agogwasvcfMessage fix in get_ld_proxies()
- 1y agogtfstoolsSupports canonical GTFS validator v5 and v6
- 1y agogtfstoolsAccepts GTFS objects from gtfsio and tidytransit ⚡
- 2y agogwasvcfgwasvcf_to_summaryset() bridges to gwasglue2
- 3y agogtfstoolsValidation delegated to MobilityData's canonical validator
- 4y agogtfstoolsAdds time-of-day, weekday and frequency filtering functions
- 4y agogtfstoolsEstablishes the core GTFS filtering and sf conversion family
Frequently asked questions
What is the difference between gtfstools and gwasvcf?
They serve adjacent needs but don't currently overlap on shipped themes. gtfstools and gwasvcf 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 gtfstools better than gwasvcf?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. gtfstools and gwasvcf 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 gtfstools?
Top gtfstools alternatives in Analytics are ranked by recent ship velocity. Browse the "gtfstools alternatives" section above for the current picks, or visit /alternatives/gtfstools-r for the full list with editorial commentary on each.
What are the best alternatives to gwasvcf?
Top gwasvcf alternatives in Analytics are ranked by recent ship velocity. Browse the "gwasvcf alternatives" section above for the current picks, or visit /alternatives/gwasvcf for the full list with editorial commentary on each.