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Bioconductor - xcore

xcore

This is the released version of xcore; for the devel version, see xcore.

xcore expression regulators inference

Bioconductor version: Release (3.21)

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 MigdaÅ [aut, cre] ORCID: 0000-0002-8021-7263 , BogumiÅ Kaczkowski [aut] ORCID: 0000-0001-6554-5608

Maintainer: Maciej MigdaÅ <mcjmigdal at gmail.com>

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

To install this package, start R (version "4.5") 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")

Details biocViews Epigenetics, GeneExpression, GeneRegulation, Regression, Sequencing, Software Version 1.12.0 In Bioconductor since BioC 3.15 (R-4.2) (3 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 URL See More 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 Enhances Depends On Me Imports Me Suggests Me xcoredata Links To Me Build Report Build Report Package Archives

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

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