h5vc
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see h5vc.
Managing alignment tallies using a hdf5 backend
Bioconductor version: 3.8
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 |
Details
| biocViews | Software |
| Version | 2.16.0 |
| 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_2.16.0.tar.gz |
| Windows Binary | h5vc_2.16.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | h5vc_2.16.0.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 |
| Old Source Packages for BioC 3.8 | Source Archive |