h5vc

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see h5vc.

Managing alignment tallies using a hdf5 backend


Bioconductor version: 3.9

This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.

Author: Paul Theodor Pyl

Maintainer: Paul Theodor Pyl <paul.theodor.pyl at gmail.com>

Citation (from within R, enter citation("h5vc")):

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("h5vc")

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("h5vc")
Building a minimal genome browser with h5vc and shiny HTML R Script
h5vc -- Tour HTML R Script
Reference Manual PDF

Details

biocViews Software
Version 2.18.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL (>= 3)
Depends grid, gridExtra, ggplot2
Imports rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools(>= 1.99.1), methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData, GenomeInfoDb
System Requirements
URL
See More
Suggests knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics
Linking To Rhtslib(>= 1.15.3)
Enhances
Depends On Me
Imports Me
Suggests Me h5vcData
Links To Me
Build Report Build Report

Package Archives

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

Source Package h5vc_2.18.0.tar.gz
Windows Binary h5vc_2.18.0.zip
Mac OS X 10.11 (El Capitan) h5vc_2.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/h5vc
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/h5vc
Bioc Package Browser https://code.bioconductor.org/browse/h5vc/
Package Short Url https://bioconductor.org/packages/h5vc/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive