xCell2
This is the development version of xCell2; for the stable release version, see xCell2.
A Tool for Generic Cell Type Enrichment Analysis
Bioconductor version: Development (3.24)
xCell2 provides methods for cell type enrichment analysis using cell type signatures. It includes three main functions - 1. xCell2Train for training custom references objects from bulk or single-cell RNA-seq datasets. 2. xCell2Analysis for conducting the cell type enrichment analysis using the custom reference. 3. xCell2GetLineage for identifying dependencies between different cell types using ontology.
Author: Almog Angel [aut, cre] 
, Dvir Aran [aut]
Maintainer: Almog Angel <almog.angel at campus.technion.ac.il>
citation("xCell2")):Almog Angel, Dvir Aran. xCell2: A Tool for Generic Cell Type Enrichment Analysis. doi:10.18129/B9.bioc.xCell2, R package version 1.5.0, https://bioconductor.org/packages/xCell2.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("xCell2")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("xCell2")| Introduction to xCell2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, RNASeq, SingleCell, Software, Transcriptomics |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.0.0) |
| Imports | SummarizedExperiment, SingleCellExperiment, Rfast, singscore, AnnotationHub, ontologyIndex, tibble, dplyr, BiocParallel, Matrix, minpack.lm, pracma, methods, readr, magrittr, progress, quadprog |
| System Requirements | |
| URL | https://github.com/AlmogAngel/xCell2 |
| Bug Reports | https://github.com/AlmogAngel/xCell2/issues |
See More
| Suggests | testthat, knitr, rmarkdown, ggplot2, randomForest, tidyr, EnhancedVolcano, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | VISTA |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | xCell2_1.5.0.tar.gz |
| Windows Binary (x86_64) | xCell2_1.5.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | xCell2_1.5.0.tgz |
| macOS Binary (sonoma-arm64) | xCell2_1.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/xCell2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/xCell2 |
| Package Short Url | https://bioconductor.org/packages/xCell2/ |
| Package Downloads Report | Download Stats |