contiBAIT

DOI: 10.18129/B9.bioc.contiBAIT  

Improves Early Build Genome Assemblies using Strand-Seq Data

Bioconductor version: Release (3.16)

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>

Citation (from within R, enter citation("contiBAIT")):

Installation

To install this package, start R (version "4.2") 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")

 

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Details

biocViews CellBasedAssays, Genetics, GenomeAssembly, ImmunoOncology, QualityControl, Software, WholeGenome
Version 1.26.0
In Bioconductor since BioC 3.3 (R-3.3) (7 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
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Build Report  

Package Archives

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

Source Package contiBAIT_1.26.0.tar.gz
Windows Binary contiBAIT_1.26.0.zip (64-bit only)
macOS Binary (x86_64) contiBAIT_1.26.0.tgz
macOS Binary (arm64) contiBAIT_1.26.0.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

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