emBALVI

0.1.0

EM Bayesian Adaptive LASSO Variational Inference Based GWAS

0packages depend

1.3Kdownloads / year

0.0%test coverage

13/13checks pass

Overview

About

Maintained by Prakash KumarFirst published 2026-04-161 releasesCRAN page ↗

Performs Genome-Wide Association Study (GWAS) analysis using Expectation-Maximization Bayesian Adaptive LASSO with Variational Inference (emBALVI). Includes genotype preprocessing, genomic relationship matrix construction, GWAS analysis, Manhattan and QQ plotting.s.

Install

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

install.packages("emBALVI", 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-embalvi

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-emBALVI

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-emBALVI

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 54 s · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.06

0.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-17
3 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 45 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: not tracked
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

1.3K

CRAN downloads in the past year

Rank #9,273 · ~4/day · ~109/mo

Releases R versions

Daily download trend is not available in this view yet.

27130 days

1.2K90 days

1.3K1 year

Compare downloads with other packages →

Also on21 r2u22 autocran

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (2)

ggplot2 RColorBrewer

LinkingTo (0)

none

Suggests (3)

rmarkdown testthat roxygen2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 302 (69%)Rd 134 (31%)

Code characteristics

Cyclomatic complexity: 4.0 median / 5 max
Test cases: 1 / 0.06 per code line

Test coverage

Line coverage

Expression

0.0%

Tests / Examples

0.0% / 0% ex

Functions

5 5 exported

Complexity

3.2 avg / 5 max

Call network

5 nodes / 0 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

5 functions

Function	Cyclo	Coverage
buildGRM exp	1	0%
convert_to_dosage exp	5	0%
emBALVI exp	4	0%
plot_manhattan exp	4	0%
plot_qq exp	2	0%

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
phenotypes_potatoyield	data.frame	192 × 2	–
snp_NN_10_hmp	data.frame	1,202 × 193	–

People & History

People (7)

Maintainer (1)

Prakash Kumar

Author, Maintainer

Authors (7)

Author, Maintainer

Author

Author

Author

Author

Author

Author

Listed in earlier versions (4)

Amrit Kumar

no longer listed · 0.1.0

Ranjit Kumar

no longer listed · 0.1.0

Sunil Kumar

no longer listed · 0.1.0

Himadri Sekhar

no longer listed · 0.1.0

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-04-16 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-16
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0
Bundled data: 718 KB / 4 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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