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