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Bioconductor - xCell2 (development version)

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 (3.22)

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] ORCID: 0009-0001-3297-6935 , Dvir Aran [aut] ORCID: 0000-0001-6334-5039

Maintainer: Almog Angel <almog.angel at campus.technion.ac.il>

Citation (from within R, enter citation("xCell2")): 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("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")
Details biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, RNASeq, SingleCell, Software, Transcriptomics Version 1.1.0 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) 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 Package Archives

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

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