Package: omicsTools 2.0.0

omicsTools: Omics Data Processing Toolbox

Provides tools for processing and analyzing omics data from genomics, transcriptomics, proteomics, and metabolomics platforms. Includes data import, filtering, imputation, normalization, targeted calibration, spectrum export, visualization, statistical comparisons, and reproducible QC reports. 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>.

Authors:Yaoxiang Li [aut], Meth Jayatilake [aut], Anushka Dongaonkar [aut], Rupayan Mallick [aut], Amrita Cheema [cre, aut]

omicsTools_2.0.0.tar.gz
omicsTools_2.0.0.zip(r-4.7-any)omicsTools_2.0.0.zip(r-4.6-any)omicsTools_2.0.0.zip(r-4.5-any)
omicsTools_2.0.0.tgz(r-4.6-any)omicsTools_2.0.0.tgz(r-4.5-any)
omicsTools_2.0.0.tar.gz(r-4.7-any)omicsTools_2.0.0.tar.gz(r-4.6-any)
omicsTools_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
omicsTools/json (API)

# Install 'omicsTools' in R:

install.packages('omicsTools', repos = c('https://cheemalab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cheemalab/omicstools/issues

On CRAN:

4.40 score 5 stars 7 scripts 264 downloads 42 exports 82 dependencies

Last updated from:692a278f8b. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	191
source / vignettes	OK	197
linux-release	OK	154
macos-release	OK	119
macos-oldrel	OK	104
windows-devel	OK	104
windows-release	OK	113
windows-oldrel	OK	102
wasm-release	OK	120

Exports:calculate_qc_rsd check_and_sort_columns check_match combine_logical_tibbles compare_omics_groups convert_mrm_data detect_duplicates detect_sample_outliers export_omics_results filter_blank_features filter_missing_value filter_qc_rsd fit_targeted_calibration flag_underexpressed_features generate_process_report generate_sample_metadata handle_missing_values impute_half_min internal_standard_normalize load_data load_omics_data load_parse_sciex_txt ms1_annotation omics_example_file omics_gui_capabilities plot_lcms_features plot_lipid_data_summary plot_met_data_summary plot_omics_heatmap plot_omics_pca plot_peak_list plot_targeted_calibration pqn_normalize predict_targeted_calibration process_mrm_duplicates process_omics_data qc_normalize run_app save_msp transpose_df validate_omics_data write_omics_report

Dependencies:askpass base64enc bit bit64 bs4Dash bslib cachem cli clipr commonmark cpp11 crayon crosstalk curl digest dplyr DT evaluate farver fastmap fontawesome fresh fs generics ggplot2 glue gtable highr hms htmltools htmlwidgets httpuv httr isoband jquerylib jsonlite knitr labeling later lazyeval lifecycle magrittr memoise mime openssl otel pillar pkgconfig prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp readr rlang rmarkdown rstudioapi S7 sass scales shiny sourcetools stringi stringr sys tibble tidyr tidyselect tinytex tzdb utf8 vctrs viridisLite vroom waiter withr xfun xtable yaml

omicsTools Workflow

Rendered fromexample_usage.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-11-04

Help page	Topics
Calculate QC Statistics and RSD	calculate_qc_rsd
Check and Sort Columns, Compare Values	check_and_sort_columns
Check Match	check_match
Combine Multiple Logical Tibbles with Intersection or Union	combine_logical_tibbles
Compare two groups of samples	compare_omics_groups
Convert MRM Data to Wide Format	convert_mrm_data
Detect Duplicate MRM Transitions	detect_duplicates
Detect multivariate sample outliers	detect_sample_outliers
Export a complete workflow result	export_omics_results
Filter features against blank samples	filter_blank_features
Filter features by missing-value rate	filter_missing_value
Filter features by quality-control relative standard deviation	filter_qc_rsd
Fit a targeted-assay calibration model	fit_targeted_calibration
Flag Underexpressed Features in Samples Based on Blank Samples	flag_underexpressed_features
Generate Process Report for Sciex 7500/5500 Raw Data	generate_process_report
Generate sample metadata from file or sample names	generate_sample_metadata
Handle Missing Values in a Tibble	handle_missing_values
Impute missing values with half of a feature minimum	impute_half_min
Internal Standard Normalize	internal_standard_normalize
Load omics data	load_data
Load an omics dataset	load_omics_data
Load and Parse SCIEX OS Exported LC-MRM-MS2 Data	load_parse_sciex_txt
Annotate MS1 mass-to-charge values	ms1_annotation
Locate a bundled plot example	omics_example_file
Available omicsTools workflows	omics_gui_capabilities
Plot detected LC-MS features by retention time and m/z	plot_lcms_features
Plot and Analyze Lipid Class Data	plot_lipid_data_summary
Plot and Analyze Metabolomics Data Summary	plot_met_data_summary
Plot a feature intensity heatmap	plot_omics_heatmap
Compute and plot principal components for omics data	plot_omics_pca
Plot a tandem mass spectrum	plot_peak_list
Plot a targeted calibration curve	plot_targeted_calibration
Perform Probabilistic Quotient Normalization for intensities	pqn_normalize
Predict concentrations with a targeted calibration model	predict_targeted_calibration
Process All MRM Transitions for Duplicates	process_mrm_duplicates
Process an omics feature table	process_omics_data
QC-RLSC Normalize function	qc_normalize
Run the omicsTools application	run_app
Write a spectrum in MSP format	save_msp
Transpose a feature table using its first column as identifiers	transpose_df
Validate and align omics tables	validate_omics_data
Write a self-contained workflow QC report	write_omics_report

Package: omicsTools 2.0.0

omicsTools: Omics Data Processing Toolbox

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