CelliD

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see CelliD.

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Bioconductor version: 3.14

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.tech at gmail.com>

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

Installation

To install this package, start R (version "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ATACSeq, Clustering, DimensionReduction, GeneExpression, GeneSetEnrichment, RNASeq, SingleCell, Software

Version 1.2.1

In Bioconductor since BioC 3.13 (R-4.1) (3 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

System Requirements

URL

Suggests knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel

Linking To Rcpp, RcppArmadillo

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package CelliD_1.2.1.tar.gz

Windows Binary CelliD_1.2.1.zip (32- & 64-bit)

macOS 10.13 (High Sierra) CelliD_1.2.1.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 3.14 Source Archive