scAnnotatR

This is the released version of scAnnotatR; for the devel version, see scAnnotatR.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14

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

Bioconductor version: Release (3.23)

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

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

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

Vy Nguyen. scAnnotatR: Pretrained learning models for cell type prediction on single cell RNA-sequencing data. doi:10.18129/B9.bioc.scAnnotatR, R package version 1.18.0, https://bioconductor.org/packages/scAnnotatR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.18.0
In Bioconductor since	BioC 3.14 (R-4.1) (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
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, r-universe

Package Archives

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

Source Package	scAnnotatR_1.18.0.tar.gz
Windows Binary (x86_64)	scAnnotatR_1.18.0.zip
macOS Binary (big-sur-x86_64)	scAnnotatR_1.18.0.tgz
macOS Binary (sonoma-arm64)	scAnnotatR_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scAnnotatR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scAnnotatR
Package Short Url	https://bioconductor.org/packages/scAnnotatR/
Package Downloads Report	Download Stats