xcore

DOI: 10.18129/B9.bioc.xcore    

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

xcore expression regulators inference

Bioconductor version: Development (3.17)

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 "4.3") 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")

 

HTML R Script xcore vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Epigenetics, GeneExpression, GeneRegulation, Regression, Sequencing, Software
Version 1.3.0
In Bioconductor since BioC 3.15 (R-4.2) (0.5 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
LinkingTo
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
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me xcoredata
Links To Me
Build Report  

Package Archives

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

Source Package xcore_1.3.0.tar.gz
Windows Binary
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/xcore/
Package Downloads Report Download Stats

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