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Bioconductor - clustifyr (development version)

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 (3.22)

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 [cre, aut], Kent Riemondy [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: Rui Fu <ray.sinensis at gmail.com>

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

To install this package, start R (version "4.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("clustifyr")
Details biocViews Annotation, GeneExpression, Microarray, Sequencing, SingleCell, Software Version 1.21.0 In Bioconductor since BioC 3.11 (R-4.0) (5 years) License MIT + file LICENSE Depends R (>= 2.10) 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 See More 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.

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