To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("h5vc")
In most cases, you don't need to download the package archive at all.
h5vc
|
This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see h5vc.
Managing alignment tallies using a hdf5 backend
Bioconductor version: 2.13
This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files. For detail see the webpage at http://www.ebi.ac.uk/~pyl/h5vc.
Author: Paul Theodor Pyl
Maintainer: Paul Theodor Pyl <pyl at embl.de>
Citation (from within R,
enter citation("h5vc")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("h5vc")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("h5vc")
| HTML | R Script | Advanced analyses |
| HTML | R Script | Building a minimal genome browser with h5vc and shiny |
| HTML | Creating Tallies with h5py/Python | |
| HTML | R Script | Creating Tallies within R |
| HTML | R Script | Scalable nucleotide tallies with HDF5 |
| Reference Manual |
Details
| biocViews | Software |
| Version | 1.0.6 |
| In Bioconductor since | BioC 2.13 (R-3.0) (2.5 years) |
| License | GPL (>= 3) |
| Depends | |
| Imports | rhdf5, ggplot2, reshape, bit64, IRanges, GenomicRanges, Biostrings |
| LinkingTo | |
| Suggests | knitr, locfit, deepSNV, BSgenome.Hsapiens.UCSC.hg19, h5vcData |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | h5vcData |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | h5vc_1.0.6.tar.gz |
| Windows Binary | h5vc_1.0.6.zip |
| Mac OS X 10.6 (Snow Leopard) | h5vc_1.0.6.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/h5vc/tree/release-2.13 |
| Package Short Url | http://bioconductor.org/packages/h5vc/ |
| Package Downloads Report | Download Stats |
Documentation »
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