README.md

In grisslab/scClassifR: Pretrained learning models for cell type prediction on single cell RNA-sequencing data

Deprecation Notice

This package was renamed to scAnnotatR.

The current version of this package is available on the scAnnotatR GitHub page: https://github.com/grisslab/scAnnotatR

scClassifR

The scClassifR package automatically classifies cells in scRNA-seq datasets. It is simple to use with a clear infrastructure to easily add additional cell type classification models. scClassifR support both Seurat and SingleCellExperiment objects as input.

Installation

You can install the latest version directly from GitHub using the devtools package:

# install devtools if needed
if (!require(devtools)) {
  install.packages("devtools")
}

# install the ReactomeGSA package
if (!require(scClassifR)) {
  install_github("grisslab/scClassifR")
}

Help

The complete usage is shown in the vignettes:

• Basic classification of cells
• Basic training of a new cell classification model
• Training of child-celltype models

For more questions / feedback please simply post an Issue.

grisslab/scClassifR documentation built on Oct. 27, 2021, 12:13 p.m.