To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("h5vc")
In most cases, you don't need to download the package archive at all.
h5vc
Managing alignment tallies using a hdf5 backend
Bioconductor version: 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>
Citation (from within R,
enter citation("h5vc")):
Installation
To install this package, start R and enter:
source("http://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 | Building a minimal genome browser with h5vc and shiny |
| HTML | R Script | h5vc -- Tour |
| Reference Manual |
Details
| biocViews | Software |
| Version | 2.0.6 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | GPL (>= 3) |
| Depends | grid, gridExtra, ggplot2 |
| Imports | rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools, methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData, GenomeInfoDb |
| LinkingTo | |
| Suggests | knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, bit64, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38 |
| 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_2.0.6.tar.gz |
| Windows Binary | h5vc_2.0.6.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | h5vc_2.0.6.tgz |
| Mac OS X 10.9 (Mavericks) | h5vc_2.0.6.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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