OmicsKit

OmicsKit is an R package that streamlines multi-omics analyses in genomics, transcriptomics, proteomics, and methylomics by simplifying data handling, generating publication-quality visualizations, and offering flexible utilities to accelerate end-to-end analysis.

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Developed by

• David R. Requena Anicama, PhD

  • Author’s name: David Requena
  • Google Scholar
  • ORCID: 0000-0002-5968-1133

• Daniel F. Guevara Díaz, BSc

  • Author’s name: Daniel F. Guevara-Diaz
  • Google Scholar
  • ORCID: 0009-0001-2786-8729

• Daniel E. Garbozo Santillan, BSc

  • Author’s name: Daniel E. Garbozo
  • Google Scholar
  • ORCID: 0009-0003-2495-6568

• Angela D. C. Alarcon Guerrero, BSc(s)

  • Author’s name: Angela D. C. Alarcon Guerrero
  • Google Scholar
  • ORCID: 0000-0003-0293-5603

License

CC BY-NC-SA 4.0

Contact

david.requena@nyulangone.org

Installation

Install the dependencies with the following:

# Install CRAN packages
install.packages("ggplot2")
install.packages("dplyr")
install.packages("stats")
install.packages("matrixStats")
install.packages("umap")
install.packages("tsne")
install.packages("magrittr")
install.packages("rlang")
install.packages("tibble")
install.packages("remotes")

You can install the development version of OmicsKit from GitHub with:

# Install from GitHub
remotes::install_github("BigMindLab/OmicsKit")

# Call library for usage
library("OmicsKit")

For a more detailed Differential Expression Analysis workflow using the OmicsKit suite, see BigMind’s GitHub organization and its custom DESeq2 pipeline.