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 meduniwien.ac.at>
citation("scAnnotatR")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, GeneExpression, SingleCell, Software, SupportVectorMachine, Transcriptomics |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2.5 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 |
See More
| 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_1.4.0.tar.gz |
| Windows Binary | scAnnotatR_1.4.0.zip |
| macOS Binary (x86_64) | scAnnotatR_1.4.0.tgz |
| macOS Binary (arm64) | scAnnotatR_1.4.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |