clustifyr

DOI: 10.18129/B9.bioc.clustifyr  

Classifier for Single-cell RNA-seq Using Cell Clusters

Bioconductor version: Release (3.16)

Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment.

Author: Rui Fu [aut], Kent Riemondy [cre, aut], Austin Gillen [ctb], Chengzhe Tian [ctb], Jay Hesselberth [ctb], Yue Hao [ctb], Michelle Daya [ctb], Sidhant Puntambekar [ctb], RNA Bioscience Initiative [fnd, cph]

Maintainer: Kent Riemondy <kent.riemondy at cuanschutz.edu>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("clustifyr")

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("clustifyr")

 

HTML	R Script	geo-annotations
HTML	R Script	Introduction to clustifyr
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Annotation, GeneExpression, Microarray, Sequencing, SingleCell, Software
Version	1.10.0
In Bioconductor since	BioC 3.11 (R-4.0) (3 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0)
Imports	cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, readr, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, matrixStats, S4Vectors, proxy, httr, utils
LinkingTo
Suggests	ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, Seurat, gprofiler2, purrr
SystemRequirements
Enhances
URL	https://github.com/rnabioco/clustifyr https://rnabioco.github.io/clustifyr/
BugReports	https://github.com/rnabioco/clustifyr/issues
Depends On Me
Imports Me
Suggests Me	clustifyrdatahub
Links To Me
Build Report

Package Archives

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

Source Package	clustifyr_1.10.0.tar.gz
Windows Binary	clustifyr_1.10.0.zip
macOS Binary (x86_64)	clustifyr_1.10.0.tgz
macOS Binary (arm64)	clustifyr_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/clustifyr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/clustifyr
Bioc Package Browser	https://code.bioconductor.org/browse/clustifyr/
Package Short Url	https://bioconductor.org/packages/clustifyr/
Package Downloads Report	Download Stats