easybio: Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit

Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker 3.0' database <https://bio-bigdata.hrbmu.edu.cn/CellMarker/>. Streamlines biological label assignment in single-cell RNA-seq data and facilitates transcriptomic analysis, including preparation of TCGA<https://portal.gdc.cancer.gov/> and GEO<https://www.ncbi.nlm.nih.gov/geo/> datasets, differential expression analysis and visualization of enrichment analysis results. Additional utility functions support various bioinformatics workflows. See Wei Cui (2024) <doi:10.1101/2024.09.14.609619> for more details.

Version: 1.3.0
Depends: R (≥ 4.1.0)
Imports: data.table (≥ 1.15.0), checkmate, ggplot2, httr2, lifecycle, R6, xml2
Suggests: litedown, patchwork, ggrepel, Seurat, limma, GEOquery, fgsea, BiocParallel, edgeR, testthat (≥ 3.0.0)
Published: 2026-10-07
DOI: 10.32614/CRAN.package.easybio
Author: Wei Cui ORCID iD [aut, cre, cph]
Maintainer: Wei Cui <m2c.w at outlook.com>
BugReports: https://github.com/person-c/easybio/issues
License: MIT + file LICENSE
URL: https://github.com/person-c/easybio
NeedsCompilation: no
Language: en-US
Citation: easybio citation info
Materials: README, NEWS
CRAN checks: easybio results

Documentation:

Reference manual: easybio.html , easybio.pdf
Vignettes: Exploratory Data Visualization with Artist (source, R code)
Example Workflow for Single-Cell Annotation with easybio (source, R code)
Example Workflow for Bulk RNA-seq Analysis with limma-voom (source, R code)

Downloads:

Package source: easybio_1.3.0.tar.gz
Windows binaries: r-devel: easybio_1.2.3.zip, r-release: easybio_1.2.3.zip, r-oldrel: easybio_1.3.0.zip
macOS binaries: r-release (arm64): easybio_1.3.0.tgz, r-oldrel (arm64): easybio_1.2.3.tgz, r-release (x86_64): easybio_1.3.0.tgz, r-oldrel (x86_64): easybio_1.3.0.tgz
Old sources: easybio archive

Linking:

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