clustifyr

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see clustifyr.

Classifier for Single-cell RNA-seq Using Cell Clusters

Bioconductor version: 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>

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

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")

geo-annotations HTML R Script

Introduction to clustifyr HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, GeneExpression, Microarray, Sequencing, SingleCell, Software

Version 1.10.0

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, readr, 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

Suggests ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, Seurat, gprofiler2, purrr

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