lilikoi

2.1.1

Metabolomics Personalized Pathway Analysis Tool

0packages depend

3.2Kdownloads / 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")

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

Release

# one-time r2u setup for Ubuntu (noble)

curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash

# then install

sudo apt install r-cran-lilikoi

Fast Ubuntu binaries via r2u (no compilation). Run the setup once per machine.

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

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

Downloads

3.2K

CRAN downloads in the past year

Rank #11,544 · ~9/day · ~270/mo

Releases R versions

lilikoi

Daily download trend is not available in this view yet.

Compare downloads with other packages →

41030 days

91890 days

3.2K1 year

Also on111 r2u

Source & community

Repository stars, issues, and contributor activity are not tracked yet.

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 MLmetrics parallel baseprincurve pathview plyr preprocessCore pROC RCy3 reticulate reshape RWeka scales stats basestringr survminer survival base

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code

3,018Lines of code

11Exported functions

Code & tests

Open call graph →

Line coverage

–

Expression

–

Tests / Examples

–

Functions

11 11 exported

Complexity

15.2 avg / 75 max

Call network

11 nodes / 0 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

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

Authors (5)

Author

Author

Author

Author

Author

Release 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
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 ↗
2.0.2
2020-10-03 · diff ↗
2.0.1
2020-08-24 · diff ↗
2.0.0
2020-07-03 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.1.0
2018-07-30

Package metadata

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