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contiBAIT

Improves Early Build Genome Assemblies using Strand-Seq Data


Bioconductor version: Release (3.18)

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 "4.3") 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")
flowBi PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews CellBasedAssays, Genetics, GenomeAssembly, ImmunoOncology, QualityControl, Software, WholeGenome
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
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Package Archives

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

Source Package contiBAIT_1.30.0.tar.gz
Windows Binary contiBAIT_1.30.0.zip
macOS Binary (x86_64) contiBAIT_1.30.0.tgz
macOS Binary (arm64) contiBAIT_1.30.0.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/
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