xcore
xcore expression regulators inference
Bioconductor version: 3.23 · Package version: 1.16.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("xcore")Details
| Maintainer | Maciej Migdał <mcjmigdal@gmail.com> |
| Author | Maciej Migdał [aut, cre] (ORCID: <https://orcid.org/0000-0002-8021-7263>), Bogumił Kaczkowski [aut] (ORCID: <https://orcid.org/0000-0001-6554-5608>) |
| License | GPL-2 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Epigenetics, GeneExpression, GeneRegulation, Regression, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/xcore/ |
Citation
From within R, enter citation("xcore"):
Maciej Migdał, Bogumił Kaczkowski. xcore: xcore expression regulators inference. doi:10.18129/B9.bioc.xcore, R package version 1.16.0, https://bioconductor.org/packages/xcore.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | xcore_1.16.0.tar.gz |
| Windows binary (x86_64) | xcore_1.16.0.zip |
| macOS binary (arm64) | xcore_1.16.0.tgz |
| macOS binary (x86_64) | xcore_1.16.0.tgz |
Dependencies
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
Reverse dependencies
Suggests Me (1): xcoredata