h5vc

This is the released version of h5vc; for the devel version, see h5vc.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

Managing alignment tallies using a hdf5 backend

Bioconductor version: Release (3.23)

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")):

Paul Theodor Pyl. h5vc: Managing alignment tallies using a hdf5 backend. doi:10.18129/B9.bioc.h5vc, R package version 2.46.0, https://bioconductor.org/packages/h5vc.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Software
Version	2.46.0
In Bioconductor since	BioC 2.13 (R-3.0) (13 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

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, r-universe

Package Archives

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

Source Package	h5vc_2.46.0.tar.gz
Windows Binary (x86_64)	h5vc_2.46.0.zip
macOS Binary (big-sur-x86_64)	h5vc_2.46.0.tgz
macOS Binary (sonoma-arm64)	h5vc_2.46.0.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