h5vc
This is the released version of h5vc; for the devel version, see h5vc.
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("h5vc")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
See More
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/h5vc/ |
| Package Short Url | https://bioconductor.org/packages/h5vc/ |
| Package Downloads Report | Download Stats |