clustifyr

This is the development version of clustifyr; for the stable release version, see clustifyr.

Classifier for Single-cell RNA-seq Using Cell Clusters

Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("clustifyr")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, GeneExpression, Microarray, Sequencing, SingleCell, Software
Version	1.15.3
In Bioconductor since	BioC 3.11 (R-4.0) (4 years)
License	MIT + file LICENSE
Depends
Imports	cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, SeuratObject, matrixStats, S4Vectors, proxy, httr, utils
System Requirements
URL	https://github.com/rnabioco/clustifyr https://rnabioco.github.io/clustifyr/
Bug Reports	https://github.com/rnabioco/clustifyr/issues

Suggests	ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	clustifyrdatahub
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/clustifyr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/clustifyr
Package Short Url	https://bioconductor.org/packages/clustifyr/
Package Downloads Report	Download Stats