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.">

easybio: Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit (original) (raw)

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: 1.1.1
Depends: R (≥ 4.1.0)
Imports: data.table, ggplot2, httr2, R6, xml2
Suggests: knitr, patchwork, rmarkdown, ggrepel, Seurat, limma, GEOquery, fgsea, edgeR, testthat (≥ 3.0.0)
Published: 2025-02-12
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
URL: https://github.com/person-c/easybio
NeedsCompilation: no
Language: en-US
Citation: easybio citation info
Materials: README NEWS
CRAN checks: easybio results

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