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h5vc

This is the development version of h5vc; for the stable release version, see h5vc.

Managing alignment tallies using a hdf5 backend

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.35.0
In Bioconductor since BioC 2.13 (R-3.0) (10 years)
License GPL (>= 3)
Depends grid, gridExtra, ggplot2
Imports rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools(>= 2.13.1), methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData, GenomeInfoDb
Linking To Rhtslib(>= 1.99.1)
Suggests knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown
System Requirements GNU make
Enhances
URL
See More
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_2.35.0.tar.gz
Windows Binary h5vc_2.35.0.zip (64-bit only)
macOS Binary (x86_64) h5vc_2.35.0.tgz
macOS Binary (arm64) h5vc_2.35.0.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