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xcore

This is the development version of xcore; for the stable release version, see xcore.

xcore expression regulators inference


Bioconductor version: Development (3.19)

xcore is an R package for transcription factor activity modeling based on known molecular signatures and user's gene expression data. Accompanying xcoredata package provides a collection of molecular signatures, constructed from publicly available ChiP-seq experiments. xcore use ridge regression to model changes in expression as a linear combination of molecular signatures and find their unknown activities. Obtained, estimates can be further tested for significance to select molecular signatures with the highest predicted effect on the observed expression changes.

Author: Maciej Migdał [aut, cre] , Bogumił Kaczkowski [aut]

Maintainer: Maciej Migdał <mcjmigdal at gmail.com>

Citation (from within R, enter citation("xcore")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("xcore")

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("xcore")
xcore vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Epigenetics, GeneExpression, GeneRegulation, Regression, Sequencing, Software
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-2
Depends R (>= 4.2)
Imports DelayedArray(>= 0.18.0), edgeR(>= 3.34.1), foreach (>= 1.5.1), GenomicRanges(>= 1.44.0), glmnet (>= 4.1.2), IRanges(>= 2.26.0), iterators (>= 1.0.13), magrittr (>= 2.0.1), Matrix (>= 1.3.4), methods (>= 4.1.1), MultiAssayExperiment(>= 1.18.0), stats, S4Vectors(>= 0.30.0), utils
System Requirements
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Suggests AnnotationHub(>= 3.0.2), BiocGenerics(>= 0.38.0), BiocParallel(>= 1.28), BiocStyle(>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub(>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer(>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata
Linking To
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Depends On Me
Imports Me
Suggests Me xcoredata
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Package Archives

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

Source Package xcore_1.7.0.tar.gz
Windows Binary xcore_1.7.0.zip
macOS Binary (x86_64) xcore_1.7.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/xcore
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/xcore
Bioc Package Browser https://code.bioconductor.org/browse/xcore/
Package Short Url https://bioconductor.org/packages/xcore/
Package Downloads Report Download Stats