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("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 | ||
| 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) |
| 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_1.10.0.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 |