SeqArray
Bioc currentData management of large-scale whole-genome sequence variant calls using GDS files
Release Lineage
Entered 2.12 · Apr 4, 2013
Current · Requires R 4.6
Description
Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
605 0 exported
Complexity
9.2 avg / 152 max
Call network
605 nodes / 790 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
33,766
Files
105
Compiled share
49.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
57
Internal functions
136
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
71.4%
Unsafe pattern score
3
Dep constraint coverage
11.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
27
First release
2013-09-27
Latest release
2026-05-30
Avg cadence
170 days
Cold removal rate
100%
Dep drift
16
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 45includes a package overview page
- Examples that run
- 100%43 run in a plain check
- Exported functions with examples
- 98%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 9%
NEW FEATURES
seqParallel()can load cloud-related packages on worker processes before calling the user-defined function, with backward compatibility for older gdsfmt versions
UTILITIES
- faster
seqSetFilterPos()than v1.52.0 seqApply()supports "$ref", "$alt", "$chrom_pos", "$chrom_pos_allele" and "$variant_index" as variable names, consistent withseqGetData()seqAddValue()supportsLogicalList,IntegerList,NumericListandCharacterListfrom the IRanges package as variable-length annotation data inputseqMulticoreSetup()invisibly returns the newly created cluster object when a multicore cluster is set up
From NEWS in the release
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/zhengxwen/seqarray on 2026-10-18.
The R CMD check workflow runs on Linux and macOS
GitHub Pages site last deployed 2017-05-16
Datasets
Topics
Depended on by (8)
Show all 14 packagesHide all 14 packages
Bioconductor (8)
People
- Xiuwen Zheng author maintainer
- Stephanie Gogarten author
- Cathy Laurie contributor
- David Levine contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("SeqArray")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btx145, 10.1093/bioinformatics/bts606.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.