R Observatory: Metrics for AllelicSeries version 0.1.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AllelicSeries

0.1.1.5Package record

Allelic Series Test

0packages depend

4Kdownloads / year

89.6%test coverage

13/13flavors OK

Overview

About

Maintained by Zachary McCawCRAN page ↗GitHub ↗

Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, O’Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2023) "An allelic series rare variant association test for candidate gene discovery" doi:10.1016/j.ajhg.2023.07.001.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("AllelicSeries", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("insitro/AllelicSeries")

Development version from insitro/AllelicSeries. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-allelicseries

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-AllelicSeries

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-AllelicSeries

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.9 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-02
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1.5

README· In the repository, left out of the releaseVignettesYes · 4 · dynamicNEWSYes · 100% structured · does not mention 0.1.1.5Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 35 (1 internal)includes a package overview page
Examples that run: 100%9 run in a plain check
Exported functions with examples: 50%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (4)

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #6,495 · ~11/day · ~330/mo

Releases R versions

Daily download trend is not available in this view yet.

48430 days

1.3K90 days

4K1 year

Compare downloads with other packages →

Also on379 r2u50 autocran2.8K conda_forge

How downloads are counted

Repository

insitro/allelicseries ↗Organization: insitro

14Stars

2Forks

0Open issues

0Open PRs

5Releases

33Commits

4Commit identities

33 commits · Last activity 2025-10-22 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 97%
Median days to close, 50 most recently updated closed issues: 11
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-21 · 142026-07-07 · 14

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/insitro/allelicseries on 2026-10-22.

Docs source (1)

README.Rmd

Automation and maintenance (1)

pre-commit

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing AllelicSeries adds 10 packages (9 with compiled code, 6.4 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, SKAT 1.2 MB.

Depends (0)

none

Imports (6)

CompQuadForm gluemethodsRcpp RNOmni SKAT

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (4)

knitr rmarkdown testthat withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (5)

Zachary McCaw

Author, Maintainer since 0.0.2.2 (2023)

Jianhui Gao

Contributor · added in 0.1.0.2

Christoph Klein

Contributor

Thomas Soare

Contributor · added in 0.1.1.1

insitro

Copyright holder

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.1.1.5Latest
record
2025-04-02 · current release · diff ↗ ·
added 2 exports
CollapseGeno, ContainsInt
0.1.1.2
record
2024-11-23 · diff ↗
0.1.1.1
record
2024-11-22 · diff ↗
0.1.0.2
record
2024-10-22 · diff ↗ ·
added 9 exports
ASBTSS, ASKATSS, BaselineSS, COASTSS, CalcSumstats, Counts, GenomicControl, SumCountSS, isPD
R
R 4.4.0 released · 2024-04-24
0.0.4.1
record
2023-10-06 · diff ↗
0.0.3.0
record
2023-05-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.0.2.2
record
2023-01-13
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-01-13
Total releases: 7 / 3 yrs
License: BSD_3_clause + file LICENSE OSI
Download size: 87 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("AllelicSeries")

Format

McCaw, Z., insitro, Gao, J., Klein, C., & Soare, T. (2025). AllelicSeries: Allelic Series Test (Version 0.1.1.5) [Computer software]. https://doi.org/10.32614/CRAN.package.AllelicSeries

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for AllelicSeries version 0.1.1.5 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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