R Observatory: Metrics for SKAT version 2.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SKAT

2.2.5Package record

SNP-Set (Sequence) Kernel Association Test

9packages dependsuggested by 5

38.1Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Seunggeun (Shawn) LeeCRAN page ↗

Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.

Install

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

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

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

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-skat

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-SKAT

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-SKAT

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Seunggeun (Shawn) Lee <lee7801@snu.ac.kr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Seunggeun",
                      family = "Lee",
                      role = "aut",
                      comment = "Shawn"),
               person(given = "Zhangchen",
                      family = "Zhao",
                      role = "aut"),
               person(given = c("with", "contributions", "from", "Larisa"),
                      family = "Miropolsky",
                      role = "aut"),
               person(given = "Michael",
                      family = "Wu",
                      role = "aut"),
               person(given = "Seunggeun",
                      family = "Lee",
                      role = "cre",
                      email = "lee7801@snu.ac.kr",
                      comment = "Shawn"))
as necessary.

CRAN check page ↗

Slowest check: 5.6 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-08
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-07
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.5

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 31
Examples that run: 100%13 run in a plain check
Exported functions with examples: 50%
Documented parameters: 100%
Return-value docs: 85%
Help pages citing references: 29%

Vignettes (1)

SKAT PDF

How these are measured

Downloads

38.1K

CRAN downloads in the past year

Rank #3,118 · ~104/day · ~3.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

4K90 days

38.1K1 year

Compare downloads with other packages →

Also on487 r2u4 autocran13.7K conda_forge194 c2d4u

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing SKAT adds 4 packages (3 with compiled code, 3.6 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, RSpectra 125 KB.

Depends (4)

R >= 2.13.0MatrixSPAtest RSpectra

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

9direct

3indirect

Depends 4 · Imports 5

Suggested by 5

Show all 14 packagesHide all 14 packages

Depends, Imports or LinkingTo, most downloaded first

SMUT AllelicSeries MetaSKAT GBJ FSTpackage LGEWIS LGRF ZIM4rv zfa

Suggests, most downloaded first

seqminer BGData GRAB FastKM bigQF

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (4)

Seunggeun Lee

Shawn

Zhangchen Zhao

· added in 2.0.0

with contributions from Larisa Miropolsky

· added in 1.0

Michael Wu

· added in 1.0

Maintainer since 0.75 (2011)

Listed in earlier versions (3)

Show 3 peopleHide 3 people

Larisa Miropolsky

no longer listed · 0.82 to 2.2.4

Micheal Wu

no longer listed · 0.82 to 0.95

Seunggeun (Shawn) Lee

no longer listed · 2.2.4

Releases (27)

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
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.2.5Latest
record
2023-01-15 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
2.2.4
record
2022-03-29 · diff ↗ ·
added 1 export
SKAT_ChrY
R
R 4.1.0 released · 2021-05-18
2.0.1
record
2020-10-20 · diff ↗ ·
added 7 exports
Get_Davies_PVal, Get_Lambda, Get_Liu_PVal, SKAT_Check_Method, SKAT_Optimal_Each_Q, SKAT_Optimal_PValue_Davies, SKAT_Optimal_PValue_Liu
R
R 4.0.0 released · 2020-04-24
2.0.0
record
2020-03-09 · diff ↗ ·
added 9 exports
Get_Genotypes_SSD_Sparse, SKATBinary_Robust, SKATBinary_Robust.SSD.OneSet, SKATBinary_Robust.SSD.OneSet_SetIndex, SKATBinary_Robust.SSD.All, SKAT_CommonRare_Robust, SKAT_CommonRare_Robust.SSD.OneSet, SKAT_CommonRare_Robust.SSD.OneSet_SetIndex, SKAT_CommonRare_Robust.SSD.All
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.3.2.1
record
2017-08-03 · diff ↗
1.3.2
record
2017-07-24 · diff ↗
1.3.0
record
2017-05-18 · diff ↗

Show 26 earlier eventsHide 26 earlier events

R
R 3.4.0 released · 2017-04-21
1.2.1
record
2016-06-28 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.1.4
record
2016-04-20 · diff ↗
1.1.2
record
2015-09-08 · diff ↗
1.0.9
record
2015-06-14 · diff ↗
1.0.7
record
2015-04-19 · diff ↗ ·
added 2 exports
SKAT_Null_Model_ChrX, SKAT_ChrX
R
R 3.2.0 released · 2015-04-16
1.0.1
record
2014-11-04 · diff ↗
1.0
record
2014-10-31 · diff ↗ ·
added 8 exports
SKAT_NULL_emmaX, SKATBinary, SKATBinary_Single, Get_EffectiveNumberTest, QQPlot_Adj, SKATBinary.SSD.OneSet, SKATBinary.SSD.OneSet_SetIndex, SKATBinary.SSD.All
R
R 3.1.0 released · 2014-04-10
0.95
record
2014-02-18 · diff ↗ ·
added 1 export
Read_SNP_WeightFile
0.93
record
2013-11-18 · diff ↗
0.92
record
2013-10-09 · diff ↗
0.91
record
2013-06-03 · diff ↗ ·
added 5 exports
Read_Plink_FAM_Cov, SKAT_CommonRare, SKAT_CommonRare.SSD.OneSet, SKAT_CommonRare.SSD.OneSet_SetIndex, SKAT_CommonRare.SSD.All
0.90
record
2013-05-23 · diff ↗ ·
removed 2 exports
SSD_FILE_OPEN.isOpen, SSD_FILE_OPEN.FileName

added 5 exports
Read_Plink_FAM_Cov, SKAT_CommonRare, SKAT_CommonRare.SSD.OneSet, SKAT_CommonRare.SSD.OneSet_SetIndex, SKAT_CommonRare.SSD.All
0.83
record
2013-05-09 · diff ↗ ·
added 1 export
Read_Plink_FAM_Cov
R
R 3.0.0 released · 2013-04-03
0.82
record
2013-03-02 · diff ↗ ·
added 22 exports
SKAT, Get_Logistic_Weights_MAF, Get_Logistic_Weights, Get_Resampling_Pvalue, Get_Resampling_Pvalue_1, Resampling_FWER, Resampling_FWER_1, Get_RequiredSampleSize, SKAT.SSD.OneSet, SKAT.SSD.OneSet_SetIndex, SKAT.SSD.All, SKAT_Null_Model, SKAT_Null_Model_MomentAdjust, Power_Continuous, Power_Logistic, Power_Continuous_R, Power_Logistic_R, Generate_SSD_SetID, Close_SSD, Open_SSD, Get_Genotypes_SSD, Read_Plink_FAM
0.81
record
2013-01-15 · diff ↗ ·
removed 2 exports
SSD_FILE_OPEN.isOpen, SSD_FILE_OPEN.FileName
0.79
record
2012-10-09 · diff ↗
0.78
record
2012-09-06 · diff ↗
0.77
record
2012-07-24 · diff ↗
0.76
record
2012-06-27 · diff ↗ ·
removed 5 exports
Read_Plink_FAM_Cov, SKAT_CommonRare, SKAT_CommonRare.SSD.OneSet, SKAT_CommonRare.SSD.OneSet_SetIndex, SKAT_CommonRare.SSD.All

added 2 exports
SSD_FILE_OPEN.isOpen, SSD_FILE_OPEN.FileName
0.75
record
2012-05-11
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-05-11
Total releases: 27 / 14 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.13.0
Bundled data: 403 KB / 6 files
Download size: 1.2 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SKAT")

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 SKAT version 2.2.5 [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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