scClassifR

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see scClassifR.

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


Bioconductor version: 3.13

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. scClassifR 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 meduniwien.ac.at>

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

Installation

To install this package, start R (version "4.1") and enter:


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

BiocManager::install("scClassifR")

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("scClassifR")
1. Introduction to scClassifR HTML R Script
2. Training basic model HTML R Script
3. Training child model HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Classification, GeneExpression, SingleCell, Software, SupportVectorMachine, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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, utils
System Requirements
URL
See More
Suggests knitr, scRNAseq, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package scClassifR_1.0.0.tar.gz
Windows Binary scClassifR_1.0.0.zip
macOS 10.13 (High Sierra) scClassifR_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scClassifR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scClassifR
Bioc Package Browser https://code.bioconductor.org/browse/scClassifR/
Package Short Url https://bioconductor.org/packages/scClassifR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive