lilikoi

2.1.1

Metabolomics Personalized Pathway Analysis Tool

0packages depend

3.3Kdownloads / year

–test coverage

9/13checks pass

Overview

About

Maintained by Lana GarmireFirst published 2018-07-308 releasesCRAN page ↗

A comprehensive analysis tool for metabolomics data. It consists a variety of functional modules, including several new modules: a pre-processing module for normalization and imputation, an exploratory data analysis module for dimension reduction and source of variation analysis, a classification module with the new deep-learning method and other machine-learning methods, a prognosis module with cox-PH and neural-network based Cox-nnet methods, and pathway analysis module to visualize the pathway and interpret metabolite-pathway relationships. References: H. Paul Benton http://www.metabolomics-forum.com/index.php?topic=281.0 Jeff Xia https://github.com/cangfengzhe/Metabo/blob/master/MetaboAnalyst/website/name_match.R Travers Ching, Xun Zhu, Lana X. Garmire (2018) doi:10.1371/journal.pcbi.1006076.

Install

R (CRAN)Ubuntu (r2u)

install.packages("lilikoi", 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-lilikoi

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

Health

CRAN checks

2ERROR2NOTE9OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
ERROR r-oldrel-macos-arm64
ERROR r-oldrel-macos-x86_64

Slowest check: 10.5 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

ERROR2026-03-10
10 OK · 2 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE

Documentation

READMEYes · 164 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 9%

Downloads

3.3K

CRAN downloads in the past year

Rank #11,508 · ~9/day · ~271/mo

Releases R versions

Daily download trend is not available in this view yet.

28830 days

92790 days

3.3K1 year

Compare downloads with other packages →

Also on111 r2u

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (28)

car caret dplyr gbm ggplot2 glmnet h2o impute infotheo limma M3C Metrics MLmetricsparallelprincurve pathview plyr preprocessCore pROC RCy3 reticulate reshape RWeka scalesstatsstringr survminersurvival

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 2,383 (79%)Rd 466 (15%)Vignettes 169 (6%)

Code characteristics

Cyclomatic complexity: 7.0 median / 75 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

11 11 exported

Complexity

15.2 avg / 75 max

Call network

11 nodes / 0 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

People & History

People (6)

Maintainer (1)

Lana Garmire

Author, Maintainer · added in 2.0.0

Authors (6)

Lana Garmire

Author, Maintainer · added in 2.0.0

Fadhl Alakwaa

Author

Xinying Fang

Author · added in 2.0.0

Sijia Huang

Author

Yu Liu

Author · added in 2.0.0

Zhijie Ren

Author · added in 2.0.0

Package Timeline

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

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
2.1.1Latest
2023-11-13 · current release · diff ↗
unarchivedReturned to CRAN
2023-11-12
'RCyr3@BioC' was updated to become installable
archivedRemoved from CRAN
2023-11-12
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.1.0
2022-02-22 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.0.4
2021-01-15 · diff ↗
2.0.3
2020-11-10 · diff ↗
unarchivedReturned to CRAN
2020-11-10
archivedRemoved from CRAN
2020-10-22
check problems were not corrected in time '\donttest' examples
2.0.2
2020-10-03 · diff ↗
2.0.1
2020-08-24 · diff ↗

Show 10 earlier events

unarchivedReturned to CRAN
2020-08-24
removedRemoved from CRAN
Version 2.0.0 has been removed
archivedRemoved from CRAN
2020-07-22
policy violation Alleged misrepresentation of authorship and copyright
2.0.0
2020-07-03 · diff ↗
unarchivedReturned to CRAN
2020-07-03
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-04-09
check problems were not corrected despite reminders
R
R 3.6.0 released · 2019-04-26
0.1.0
2018-07-30
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-07-30
Total releases: 8 / 8 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Download size: 1.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Missing Data Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Report a problem with this page →