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 (3.21)
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("CelliD")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ATACSeq, Clustering, DimensionReduction, GeneExpression, GeneSetEnrichment, RNASeq, SingleCell, Software |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
See More
| 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_1.15.0.tar.gz |
| Windows Binary (x86_64) | CelliD_1.15.0.zip |
| macOS Binary (x86_64) | CelliD_1.15.0.tgz |
| macOS Binary (arm64) | |
| 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 |