h5vc

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see h5vc.

Managing alignment tallies using a hdf5 backend


Bioconductor version: 3.7

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 "3.5") 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 2.14.0
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(>= 1.19.38), 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 Rsamtools
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_2.14.0.tar.gz
Windows Binary h5vc_2.14.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) h5vc_2.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/h5vc
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/h5vc
Package Short Url https://bioconductor.org/packages/h5vc/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive