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>

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

Installation

To install this package, start R (version "4.0") 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")
shims in TxRegInfra HTML R Script
TxRegInfra -- classes and methods for TxRegQuery HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Network, Software
Version 1.10.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License Artistic-2.0
Depends R (>= 3.5), 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, shiny, biovizBase(>= 1.27.2), Gviz, AnnotationFilter, ensembldb, ontoProc, rjson, graph, TFutils(>= 1.5.4)
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Depends On Me
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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
Old Source Packages for BioC 3.12 Source Archive