causalASCEND
This is the development version of causalASCEND; to use it, please install the devel version of Bioconductor.
Scalable Two-Tier Causal Discovery for Multi-Omic Data
Bioconductor version: Development (3.24)
Causal ASCEND (Ancestral Scalable Causal discovEry via iNherited Descent) infers ancestral (cause-before-effect) relations among downstream molecular variables, such as gene expression, when a layer of upstream variables, such as genotypes or methylation sites, is known to precede them. Each conditional independence test conditions only on a small, iteratively refined set of nearest ancestors instead of the whole upstream layer, so the number of tests grows polynomially with the number of variables. The package accepts matrices, SummarizedExperiment objects or a MultiAssayExperiment, and returns the ancestral relations with the rule and evidence behind each one.
Author: Stephen Asiedu [aut, cre] 
, David Watson [aut]
Maintainer: Stephen Asiedu <stephen.asiedu at kcl.ac.uk>
citation("causalASCEND")):Stephen Asiedu, David Watson. causalASCEND: Scalable Two-Tier Causal Discovery for Multi-Omic Data. doi:10.18129/B9.bioc.causalASCEND, R package version 0.99.5, https://bioconductor.org/packages/causalASCEND.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("causalASCEND")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("causalASCEND")| Two-tier causal discovery with causalASCEND | HTML | R Script |
| Reference Manual |
Details
| biocViews | GeneExpression, GeneticVariability, GraphAndNetwork, MultipleComparison, Network, NetworkInference, SNP, Software, SystemsBiology, Transcriptomics |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | methods, stats, SummarizedExperiment, utils |
| System Requirements | |
| URL | https://github.com/SparkAILab/causalASCEND |
| Bug Reports | https://github.com/SparkAILab/causalASCEND/issues |
See More
| Suggests | BiocStyle, knitr, MultiAssayExperiment, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | causalASCEND_0.99.5.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/causalASCEND |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/causalASCEND |
| Package Short Url | https://bioconductor.org/packages/causalASCEND/ |
| Package Downloads Report | Download Stats |