RAINBOWR

0.1.38

Genome-Wide Association Study with SNP-Set Methods

0packages depend

21.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Kosuke HamazakiFirst published 2019-11-1211 releasesCRAN page ↗

By using 'RAINBOWR' (Reliable Association INference By Optimizing Weights with R), users can test multiple SNPs (Single Nucleotide Polymorphisms) simultaneously by kernel-based (SNP-set) methods. This package can also be applied to haplotype-based GWAS (Genome-Wide Association Study). Users can test not only additive effects but also dominance and epistatic effects. In detail, please check our paper on PLOS Computational Biology: Kosuke Hamazaki and Hiroyoshi Iwata (2020) doi:10.1371/journal.pcbi.1007663.

Install

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

install.packages("RAINBOWR", 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-rainbowr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-RAINBOWR

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

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

Health

CRAN checks

13OK

Slowest check: 7.0 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,241 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 58%

Downloads

21.3K

CRAN downloads in the past year

Rank #4,727 · ~58/day · ~1.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

46030 days

1.9K90 days

21.3K1 year

Compare downloads with other packages →

Also on398 r2u

Dependencies

Declared dependencies

32 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (18)

RcppMatrixclusterMASSpbmcapply optimxmethodsape stringr pegas rrBLUP expm here htmlwidgets Rfast gaston MM4LMM R.utils

LinkingTo (2)

Rcpp RcppEigen

Suggests (16)

knitr rmarkdown plotly haplotypes adegenet ggplot2 ggtree scatterpie phylobase ggimage furrr future progressr foreach doParallel data.table

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 22,173 (68%)Rd 8,185 (25%)C++ 2,171 (7%)Vignettes 297 (1%)

Code characteristics

Cyclomatic complexity: 8.0 median / 101 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

147 56 exported

Complexity

21.6 avg / 101 max

Call network

147 nodes / 302 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Maintainer (1)

Kosuke Hamazaki

Author, Maintainer

Authors (2)

Kosuke Hamazaki

Author, Maintainer

Hiroyoshi Iwata

Author, Contributor

Contributors (1)

Hiroyoshi Iwata

Author, Contributor

Package Timeline

11 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.38Latest
2025-05-21 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.35
2024-03-03 · diff ↗
0.1.33
2023-09-12 · diff ↗
0.1.32
2023-08-09 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.29
2022-01-07 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.26
2021-02-08 · diff ↗
0.1.21
2020-10-26 · diff ↗
0.1.19
2020-07-23 · diff ↗
0.1.17
2020-04-29 · diff ↗
R
R 4.0.0 released · 2020-04-24

Show 3 earlier events

0.1.14
2019-11-14 · diff ↗
0.1.13
2019-11-12
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-11-12
Total releases: 11 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 105 KB / 2 files
Download size: 459 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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