CelliD

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Bioconductor version: Release (3.17)

CelliD is a clustering-free multivariate statistical method for the robust extraction of per-cell gene signatures from single-cell RNA-seq. CelliD allows unbiased cell identity recognition across different donors, tissues-of-origin, model organisms and single-cell omics protocols. The package can also be used to explore functional pathways enrichment in single cell data.

Author: Akira Cortal [aut, cre], Antonio Rausell [aut, ctb]

Maintainer: Akira Cortal <akira.cortal at institutimagine.org>

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CelliD")

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("CelliD")

CelliD Vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Details

biocViews	ATACSeq, Clustering, DimensionReduction, GeneExpression, GeneSetEnrichment, RNASeq, SingleCell, Software
Version	1.8.1
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment
Imports	Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater, stringr, irlba, data.table, glue, pbapply, umap, Rtsne, reticulate, fastmatch, matrixStats, ggplot2, BiocParallel, SummarizedExperiment, fgsea
Linking To	Rcpp, RcppArmadillo
Suggests	knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel
System Requirements
Enhances
URL

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CelliD_1.8.1.tar.gz
Windows Binary	CelliD_1.8.1.zip
macOS Binary (x86_64)	CelliD_1.8.1.tgz
macOS Binary (arm64)	CelliD_1.8.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CelliD
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CelliD
Bioc Package Browser	https://code.bioconductor.org/browse/CelliD/
Package Short Url	https://bioconductor.org/packages/CelliD/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive