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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/xCell2/ |
| Package Short Url | https://bioconductor.org/packages/xCell2/ |
| Package Downloads Report | Download Stats |