clustifyr
This is thereleased version of clustifyr; for the devel version, seeclustifyr.
Classifier for Single-cell RNA-seq Using Cell Clusters
Bioconductor version: Release (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] (ROR: <https://ror.org/03wmf1y16>)
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")BiocManager::install("clustifyr")For older versions of R, please refer to the appropriateBioconductor 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 | 1.22.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (5.5 years) |
| License | MIT + fileLICENSE |
| 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/clustifyrhttps://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
FollowInstallation instructions to use this package in your R session.
| Source Package | clustifyr_1.22.0.tar.gz |
| Windows Binary (x86_64) | clustifyr_1.22.0.zip |
| macOS Binary (x86_64) | clustifyr_1.22.0.tgz |
| macOS Binary (arm64) | clustifyr_1.22.0.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 |