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CelliD

This is the development version of CelliD; for the stable release version, see CelliD.

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Bioconductor version: Development (3.18)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.9.0
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
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Package Archives

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

Source Package CelliD_1.9.0.tar.gz
Windows Binary CelliD_1.9.0.zip
macOS Binary (x86_64) CelliD_1.9.0.tgz
macOS Binary (arm64) CelliD_1.9.0.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