h5vc

DOI: 10.18129/B9.bioc.h5vc    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see h5vc.

Managing alignment tallies using a hdf5 backend

Bioconductor version: 3.12

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>

Installation

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

if (!requireNamespace("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")

 

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

Details

biocViews	Software
Version	2.24.0
In Bioconductor since	BioC 2.13 (R-3.0) (7.5 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
LinkingTo	Rhtslib(>= 1.15.3)
Suggests	knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics
SystemRequirements	GNU make
Enhances
URL
Depends On Me
Imports Me
Suggests Me	h5vcData
Links To Me
Build Report

Package Archives

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

Source Package	h5vc_2.24.0.tar.gz
Windows Binary	h5vc_2.24.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	h5vc_2.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/h5vc
Source Repository (Developer Access)	git clone [email protected]:packages/h5vc
Package Short Url	https://bioconductor.org/packages/h5vc/
Package Downloads Report	Download Stats