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easybio

easybio provides a comprehensive toolkit for single-cell RNA-seq annotation using the CellMarker2.0 database. It streamlines the process of assigning biological labels in scRNA-seq data, integrating seamlessly with tools like Seurat. While the package includes additional bioinformatics workflows, such as handling TCGA and GEO datasets, differential expression analysis, and enrichment analysis visualization, for details specifically on the single-cell annotation functionality, please refer to the bioRxiv preprint.

Download and Usage

You can install the development version of easybio from GitHub with:

devtools::install("person-c/easybio", build_vignettes = TRUE)

To know how to use this package, please see the wiki or run:

vignette(topic = "example-bulk-rna-seq-workflow", package = 'easybio')
vignette(topic = "example-single-cell-annotation", package = "easybio")

To learn the difference between development version and CRAN version, see NEWS

Citation

If you use the single-cell annotation functionality from easybio, consider cite:

Wei, Cui. (2024). easybio: an R Package for Single-Cell Annotation with CellMarker2.0. bioRxiv. https://doi.org/10.1101/2024.09.14.609619

C. Hu, T. Li, Y. Xu, X. Zhang, F. Li, J. Bai, J. Chen, W. Jiang, K. Yang, Q. Ou, X. Li, P. Wang, Y. Zhang, CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data, Nucleic Acids Research 51 (D1) (2022) D870–D876. doi:10.1093/nar/gkac947. https://doi.org/10.1093/nar/gkac947

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.