h5vc

Managing alignment tallies using a hdf5 backend

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("h5vc")

To cite this package in a publication, start R and enter:

    citation("h5vc")

Documentation

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 h5vc - Tour
HTML R Script Scalable nucleotide tallies with HDF5
PDF   Reference Manual

Details

biocViews Software
Version 1.3.0
In Bioconductor since BioC 2.13 (R-3.0)
License GPL (>= 3)
Depends grid, gridExtra, ggplot2
Imports rhdf5, reshape, IRanges, Biostrings, Rsamtools, methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData
Suggests knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, bit64
System Requirements
URL
Depends On Me
Imports Me Rariant
Suggests Me h5vcData, SomaticSignatures

Package Downloads

Package Source h5vc_1.3.0.tar.gz
Windows Binary h5vc_1.1.28.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) h5vc_1.3.0.tgz
Mac OS X 10.9 (Mavericks)
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