clustifyr

DOI: 10.18129/B9.bioc.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 (3.12)

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, cre], Kent Riemondy [aut], Austin Gillen [ctb], Chengzhe Tian [ctb], Jay Hesselberth [ctb], Yue Hao [ctb], Michelle Daya [ctb], Sidhant Puntambekar [ctb]

Maintainer: Rui Fu <raysinensis at gmail.com>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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

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, Microarray, Sequencing, SingleCell, Software
Version 1.1.2
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, readr, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, matrixStats, S4Vectors, proxy, httr
LinkingTo
Suggests ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle
SystemRequirements
Enhances
URL http://github.com/rnabioco/clustifyr#readme 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_1.1.2.tar.gz
Windows Binary clustifyr_1.1.2.zip
macOS 10.13 (High Sierra) clustifyr_1.1.2.tgz
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

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