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clustifyr

Classifier for Single-cell RNA-seq Using Cell Clusters


Bioconductor version: Release (3.18)

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 "4.3") 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")
geo-annotations HTML R Script
Introduction to clustifyr HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Annotation, GeneExpression, Microarray, Sequencing, SingleCell, Software
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License MIT + file LICENSE
Depends R (>= 3.5.0)
Imports cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, 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
See More
Suggests ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, Seurat, 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 clustifyr_1.14.0.tar.gz
Windows Binary clustifyr_1.14.0.zip
macOS Binary (x86_64) clustifyr_1.14.0.tgz
macOS Binary (arm64) clustifyr_1.14.0.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