R Observatory: Metrics for omicsTools version 1.1.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

omicsTools

1.1.7Package record

Omics Data Process Toolbox

0packages depend

2.8Kdownloads / year

0.2%test coverage

13/13flavors OK

Overview

About

Maintained by Yaoxiang LiCRAN page ↗

Processing and analyzing omics data from genomics, transcriptomics, proteomics, and metabolomics platforms. It provides functions for preprocessing, normalization, visualization, and statistical analysis, as well as machine learning algorithms for predictive modeling. 'omicsTools' is an essential tool for researchers working with high-throughput omics data in fields such as biology, bioinformatics, and medicine.The QC-RLSC (quality control–based robust LOESS signal correction) algorithm is used for normalization. Dunn et al. (2011) doi:10.1038/nprot.2011.335.

Install

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

install.packages("omicsTools", 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-omicstools

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-omicsTools

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-omicsTools

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

13OK

CRAN check page ↗

Slowest check: 5.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.7

READMEYes · 215 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · does not mention 1.1.7Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 38 (1 internal)
Examples that run: 79%22 run in a plain check · 6 never run
Exported functions with examples: 76%
Documented parameters: 100%
Return-value docs: 92%
Help pages citing references: 3%

Vignettes (1)

OmicsData Example Usage HTML

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #17,227 · ~8/day · ~234/mo

Releases R versions

Daily download trend is not available in this view yet.

32230 days

72890 days

2.8K1 year

Compare downloads with other packages →

Also on80 r2u8 autocran

How downloads are counted

Dependencies

Declared dependencies

51 external dependencies (excludes base and recommended)

Installing omicsTools adds 140 packages (64 with compiled code, 113 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (1)

R >= 4.1.0

Imports (36)

bs4Dash cli config dbscan dplyr DT forcats ggplot2 ggpubr ggrepel ggsci ggvenn golem janitor magrittr matrixStatsgrDevicesmethodsmoments outliers pheatmap purrr RColorBrewer readxl readr rlangstatsshiny shinycssloaders shinyWidgets stringr tibble tidyrutilsviridistools

LinkingTo (0)

none

Suggests (20)

Biobase pvca testthat knitr rmarkdown Boruta randomForest caret recipes parsnip workflows rsample tune dials doParallel vip GOplot openxlsx UpSetR zip

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Yaoxiang Li

Maintainer since 1.0.5 (2023), Author

Listed in earlier versions (3)

Show 3 peopleHide 3 people

Amrita Cheema

no longer listed · 1.0.5

Meth Jayatilake

no longer listed · 1.0.5

Zihao Zhang

no longer listed · 1.0.5

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.7Latest
record
2025-12-16 · current release · diff ↗ ·
removed 2 exports
impute, normalize

added 35 exports
calculate_cooks_distance, calculate_lof, calculate_measures, calculate_qc_rsd, check_and_sort_columns, check_match, combine_logical_tibbles, convert_mrm_data, convert_to_binary_matrix, createOmicsData, define_thresholds, detect_duplicates, ensure_enough_sets_for_upset, flag_anomalies, flag_underexpressed_features, generate_data_with_anomalies, generate_process_report, handle_missing_values, initialize_results_df, internal_standard_normalize, load_parse_sciex_txt, ms1_annotation, perform_batch_assessment, perform_feature_selection, pieDraw, plot_distribution_measures, plot_lipid_data_summary, plot_met_data_summary, plot_sample_measures, pqn_normalize and 5 more
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.5
record
2023-07-03
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-07-03
Total releases: 2 / 3 yrs
License: AGPL (>= 3) OSI · relicensed from MIT + file LICENSE in 1.1.7
Minimum R: ≥ 4.1.0
Download size: 564 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("omicsTools")

Format

Li, Y. (2025). omicsTools: Omics Data Process Toolbox (Version 1.1.7) [Computer software]. https://doi.org/10.32614/CRAN.package.omicsTools

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 omicsTools version 1.1.7 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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