TxRegInfra

DOI: 10.18129/B9.bioc.TxRegInfra    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see TxRegInfra.

Metadata management for multiomic specification of transcriptional regulatory networks

Bioconductor version: 3.12

This package provides interfaces to genomic metadata employed in regulatory network creation, with a focus on noSQL solutions. Currently quantitative representations of eQTLs, DnaseI hypersensitivity sites and digital genomic footprints are assembled using an out-of-memory extension of the RaggedExperiment API.

Author: Vince Carey

Maintainer: VJ Carey <stvjc at channing.harvard.edu>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TxRegInfra")

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("TxRegInfra")

 

HTML	R Script	shims in TxRegInfra
HTML	R Script	TxRegInfra -- classes and methods for TxRegQuery
PDF		Reference Manual
Text		NEWS

Details

biocViews	Network, Software
Version	1.10.0
In Bioconductor since	BioC 3.7 (R-3.5) (3 years)
License	Artistic-2.0
Depends	R (>= 3.5), RaggedExperiment(>= 1.3.11), mongolite
Imports	methods, rjson, GenomicRanges, IRanges, BiocParallel, GenomeInfoDb, S4Vectors, SummarizedExperiment, utils
LinkingTo
Suggests	knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, shiny, biovizBase(>= 1.27.2), Gviz, AnnotationFilter, ensembldb, ontoProc, rjson, graph, TFutils(>= 1.5.4)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	TxRegInfra_1.10.0.tar.gz
Windows Binary	TxRegInfra_1.10.0.zip
macOS 10.13 (High Sierra)	TxRegInfra_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TxRegInfra
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TxRegInfra
Package Short Url	https://bioconductor.org/packages/TxRegInfra/
Package Downloads Report	Download Stats