clustifyr
This is the released version of clustifyr; for the devel version, see clustifyr.
Classifier for Single-cell RNA-seq Using Cell Clusters
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.24.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 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_1.24.0.tar.gz |
| Windows Binary (x86_64) | clustifyr_1.24.0.zip |
| macOS Binary (big-sur-x86_64) | clustifyr_1.24.0.tgz |
| macOS Binary (sonoma-arm64) | clustifyr_1.24.0.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 |