Combining single-cell and bulk RNA-sequencing data to identify phenotype-associated cells
SCIPAC (Single- Cell and bulk data-based Identifier for Phenotype Associated Cells) is a computational method that identifies cells in single-cell data that are associated with a given phenotype. This phenotype can be binary (e.g., cancer vs. normal), ordinal (e.g., different stages of cancer), continuous (e.g., quantitative traits), or survival.
- Nov, 2022: SCIPAC version 1.0.0 is launched
- System requirements: SCIPAC is developed under R (version >= 4.1.2).
- Latest version: the latest developmental version of SCIPAC can be downloaded from GitHub and installed from source by
devtools::install_github('RavenGan/SCIPAC').
Please see http://RavenGan.github.io/SCIPAC/vignettes/introduction.html for details. In the introduction, we also include how to use TCGA databases as the source of bulk RNA-seq data for the application of SCIPAC. In the R terminal, users can also use ?SCIPAC to access the help documents.
In the SCIPAC tutorial, we use multiple examples to show the function and performance of SCIPAC. Example datasets are also included in SCIPAC package.