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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 [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 |
Reference manual: | easybio.pdf |
Vignettes: |
example-bulk-rna-seq-workflow (source, R code) example-single-cell-annotation (source, R code) |
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 |
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.