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Bioconductor - contiBAIT

contiBAIT

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see contiBAIT.

Improves Early Build Genome Assemblies using Strand-Seq Data

Bioconductor version: 3.10

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 "3.6") 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")
Details biocViews CellBasedAssays, Genetics, GenomeAssembly, ImmunoOncology, QualityControl, Software, WholeGenome Version 1.14.0 In Bioconductor since BioC 3.3 (R-3.3) (8 years) License BSD_2_clause + file LICENSE Depends 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 System Requirements URL See More Suggests BiocStyle Linking To Rcpp, BH 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.

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