xcore

DOI: 10.18129/B9.bioc.xcore    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see xcore.

xcore expression regulators inference

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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

Details

biocViews	Epigenetics, GeneExpression, GeneRegulation, Regression, Sequencing, Software
Version	1.0.0
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_1.0.0.tar.gz
Windows Binary	xcore_1.0.0.zip
macOS Binary (x86_64)	xcore_1.0.0.tgz
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