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 (3.21)
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 "4.5") 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")| 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 | 1.19.0 |
| 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_1.19.0.tar.gz |
| Windows Binary (x86_64) | clustifyr_1.19.0.zip |
| macOS Binary (x86_64) | clustifyr_1.19.0.tgz |
| macOS Binary (arm64) | clustifyr_1.19.0.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 |