DOI: 10.18129/B9.bioc.xcore  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see xcore.

xcore expression regulators inference

Bioconductor version: 3.16

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>

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biocViews Epigenetics, GeneExpression, GeneRegulation, Regression, Sequencing, Software
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (1 year)
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
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
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Source Package xcore_1.2.0.tar.gz
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