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: 1.1.0
Depends: R (≥ 2.10)
Imports: data.table, ggplot2, limma, R6
Suggests: knitr, patchwork, rmarkdown, ggrepel, Seurat, httr2, GEOquery, fgsea, edgeR, testthat (≥ 3.0.0), xml2
Published: 2024-09-16
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.pdf
Vignettes: example-bulk-rna-seq-workflow (source, R code)
example-single-cell-annotation (source, R code)

Downloads:

Package source: easybio_1.1.0.tar.gz
Windows binaries: r-devel: easybio_1.1.0.zip, r-release: easybio_1.1.0.zip, r-oldrel: easybio_1.1.0.zip
macOS binaries: r-release (arm64): easybio_1.1.0.tgz, r-oldrel (arm64): easybio_1.1.0.tgz, r-release (x86_64): easybio_1.1.0.tgz, r-oldrel (x86_64): easybio_1.1.0.tgz
Old sources: easybio archive

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