scAnnotatR

This package is for version 3.21 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: 3.21

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] ORCID iD ORCID: 0000-0003-3436-3662 , Johannes Griss [cre] ORCID iD ORCID: 0000-0003-2206-9511

Maintainer: Johannes Griss <johannes.griss at meduniwien.ac.at>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("scAnnotatR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scAnnotatR")

1. Introduction to scAnnotatR HTML R Script

2. Training basic model HTML R Script

3. Training child model HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, GeneExpression, SingleCell, Software, SupportVectorMachine, Transcriptomics

Version 1.14.0

In Bioconductor since BioC 3.14 (R-4.1) (4 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

System Requirements

URL https://github.com/grisslab/scAnnotatR

Bug Reports https://github.com/grisslab/scAnnotatR/issues/new

Suggests knitr, rmarkdown, scRNAseq, testthat

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me scAnnotatR.models

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scAnnotatR_1.14.0.tar.gz

Windows Binary (x86_64) scAnnotatR_1.14.0.zip

macOS Binary (x86_64) scAnnotatR_1.14.0.tgz

macOS Binary (arm64) scAnnotatR_1.14.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/scAnnotatR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scAnnotatR

Bioc Package Browser https://code.bioconductor.org/browse/scAnnotatR/

Package Short Url https://bioconductor.org/packages/scAnnotatR/

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