clustifyr
Classifier for Single-cell RNA-seq Using Cell Clusters
Bioconductor version: Release (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 [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("clustifyr")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Annotation, GeneExpression, Microarray, Sequencing, SingleCell, Software |
Version | 1.16.2 |
In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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.
Source Package | clustifyr_1.16.2.tar.gz |
Windows Binary | clustifyr_1.16.2.zip |
macOS Binary (x86_64) | clustifyr_1.16.2.tgz |
macOS Binary (arm64) | clustifyr_1.16.2.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 |
Old Source Packages for BioC 3.19 | Source Archive |