easybio: Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit

Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker2.0' database (see Xia Li, Peng Wang, Yunpeng Zhang (2023) <doi:10.1093/nar/gkac947>). 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:	1.2.1
Depends:	R (≥ 4.1.0)
Imports:	data.table (≥ 1.15.0), checkmate, ggplot2, httr2, R6, xml2
Suggests:	litedown, knitr, patchwork, ggrepel, Seurat, limma, GEOquery, fgsea, edgeR, testthat (≥ 3.0.0)
Published:	2025-08-30
Author:	Wei Cui [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:	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_1.2.1.tar.gz
Windows binaries:	r-devel: easybio_1.1.1.zip, r-release: easybio_1.1.1.zip, r-oldrel: easybio_1.1.1.zip
macOS binaries:	r-release (arm64): easybio_1.1.1.tgz, r-oldrel (arm64): easybio_1.1.1.tgz, r-release (x86_64): easybio_1.2.1.tgz, r-oldrel (x86_64): easybio_1.2.1.tgz
Old sources:	easybio archive

Linking:

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