CelliD
This is thereleased version of CelliD; for the devel version, seeCelliD.
Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis
Bioconductor version: Release (3.22)
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")BiocManager::install("CelliD")For older versions of R, please refer to the appropriateBioconductor 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 | 1.18.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4.5 years) |
| License | GPL-3 + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | CelliD_1.18.0.tar.gz |
| Windows Binary (x86_64) | CelliD_1.18.0.zip |
| macOS Binary (x86_64) | CelliD_1.18.0.tgz |
| macOS Binary (arm64) | CelliD_1.18.0.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 |