contiBAIT

DOI: 10.18129/B9.bioc.contiBAIT  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see contiBAIT.

Improves Early Build Genome Assemblies using Strand-Seq Data

Bioconductor version: 3.17

Using strand inheritance data from multiple single cells from the organism whose genome is to be assembled, contiBAIT can cluster unbridged contigs together into putative chromosomes, and order the contigs within those chromosomes.

Author: Kieran O'Neill, Mark Hills, Mike Gottlieb

Maintainer: Kieran O'Neill <koneill at bccrc.ca>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("contiBAIT")

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("contiBAIT")

 

PDF	R Script	flowBi
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CellBasedAssays, Genetics, GenomeAssembly, ImmunoOncology, QualityControl, Software, WholeGenome
Version	1.28.0
In Bioconductor since	BioC 3.3 (R-3.3) (7.5 years)
License	BSD_2_clause + file LICENSE
Depends	R (>= 3.5.0), BH (>= 1.51.0.3), Rsamtools(>= 1.21)
Imports	data.table, grDevices, clue, cluster, gplots, BiocGenerics(>= 0.31.6), S4Vectors, IRanges, GenomicRanges, Rcpp, TSP, GenomicFiles, gtools, rtracklayer, BiocParallel, DNAcopy, colorspace, reshape2, ggplot2, methods, exomeCopy, GenomicAlignments, diagram
LinkingTo	Rcpp, BH
Suggests	BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	contiBAIT_1.28.0.tar.gz
Windows Binary	contiBAIT_1.28.0.zip
macOS Binary (x86_64)	contiBAIT_1.28.0.tgz
macOS Binary (arm64)	contiBAIT_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/contiBAIT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/contiBAIT
Bioc Package Browser	https://code.bioconductor.org/browse/contiBAIT/
Package Short Url	https://bioconductor.org/packages/contiBAIT/
Package Downloads Report	Download Stats