DOI: 10.18129/B9.bioc.scAnnotatR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scAnnotatR.

Pretrained learning models for cell type prediction on single cell RNA-sequencing data

Bioconductor version: 3.16

The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs.

Author: Vy Nguyen [aut] , Johannes Griss [cre]

Maintainer: Johannes Griss <johannes.griss at>

Citation (from within R, enter citation("scAnnotatR")):


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HTML R Script 1. Introduction to scAnnotatR
HTML R Script 2. Training basic model
HTML R Script 3. Training child model
PDF   Reference Manual
Text   NEWS


biocViews Classification, GeneExpression, SingleCell, Software, SupportVectorMachine, Transcriptomics
Version 1.4.0
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License MIT + file LICENSE
Depends R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment
Imports dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub, utils
Suggests knitr, rmarkdown, scRNAseq, testthat
Depends On Me
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