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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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=easybio to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.