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  [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:
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