gpart
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see gpart.
Human genome partitioning of dense sequencing data by identifying haplotype blocks
Bioconductor version: 3.9
we provide a new SNP sequence partitioning method which partitions the whole SNP sequence based on not only LD block structures but also gene location information. The LD block construction for GPART is performed using Big-LD algorithm, with additional improvement from previous version reported in Kim et al.(2017). We also add a visualization tool to show the LD heatmap with the information of LD block boundaries and gene locations in the package.
Author: Sun Ah Kim [aut, cre, cph], Yun Joo Yoo [aut, cph]
Maintainer: Sun Ah Kim <sunnyeesl at gmail.com>
citation("gpart")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("gpart")
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("gpart")| Your Vignette Title | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0), grid, Homo.sapiens, TxDb.Hsapiens.UCSC.hg38.knownGene |
| Imports | igraph, biomaRt, Rcpp, data.table, OrganismDbi, AnnotationDbi, grDevices, stats, utils, GenomicRanges, IRanges |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gpart_1.2.0.tar.gz |
| Windows Binary | gpart_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | gpart_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/gpart |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gpart |
| Bioc Package Browser | https://code.bioconductor.org/browse/gpart/ |
| Package Short Url | https://bioconductor.org/packages/gpart/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |