gpart

DOI: 10.18129/B9.bioc.gpart    

Human genome partitioning of dense sequencing data by identifying haplotype blocks

Bioconductor version: Release (3.8)

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 (from within R, enter citation("gpart")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("gpart", version = "3.8")

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")

 

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Details

biocViews Clustering, Software
Version 1.0.0
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
LinkingTo Rcpp
Suggests knitr, rmarkdown, BiocStyle, testthat
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Enhances
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Depends On Me
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Package Archives

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Source Package gpart_1.0.0.tar.gz
Windows Binary gpart_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) gpart_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/gpart
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gpart
Package Short Url http://bioconductor.org/packages/gpart/
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