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h5vc

Managing alignment tallies using a hdf5 backend


Bioconductor version: Release (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")

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 2.36.0
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(>= 2.13.1), methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData, GenomeInfoDb
System Requirements GNU make
URL
See More
Suggests knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown
Linking To Rhtslib(>= 1.99.1)
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_2.36.0.tar.gz
Windows Binary h5vc_2.36.0.zip
macOS Binary (x86_64) h5vc_2.36.0.tgz
macOS Binary (arm64) h5vc_2.36.0.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