xcore
This is the development version of xcore; for the stable release version, see xcore.
xcore expression regulators inference
Bioconductor version: Development (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 Migdał [aut, cre] (ORCID:
Maintainer: Maciej Migdał <mcjmigdal at gmail.com>
citation("xcore")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | Epigenetics, GeneExpression, GeneRegulation, Regression, Sequencing, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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 |
| 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.
| Source Package | xcore_1.11.0.tar.gz |
| Windows Binary (x86_64) | xcore_1.11.0.zip (64-bit only) |
| macOS Binary (x86_64) | xcore_1.11.0.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 |