TxRegInfra

This package is for version 3.8 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: 3.8

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>

Citation (from within R, enter citation("TxRegInfra")):

Installation

To install this package, start R (version "3.5") and enter:


if (!require("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")
TxRegInfra -- classes and methods for TxRegQuery HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Network, Software
Version 1.2.1
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License Artistic-2.0
Depends RaggedExperiment(>= 1.3.11), mongolite
Imports methods, rjson, GenomicRanges, IRanges, BiocParallel, GenomeInfoDb, S4Vectors, SummarizedExperiment, utils
System Requirements
URL
See More
Suggests knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, biovizBase(>= 1.27.2), Gviz, AnnotationFilter, ensembldb
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package TxRegInfra_1.2.1.tar.gz
Windows Binary TxRegInfra_1.2.1.zip
Mac OS X 10.11 (El Capitan) TxRegInfra_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/TxRegInfra
Source Repository (Developer Access) git clone [email protected]:packages/TxRegInfra
Bioc Package Browser https://code.bioconductor.org/browse/TxRegInfra/
Package Short Url https://bioconductor.org/packages/TxRegInfra/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive