contiBAIT

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see contiBAIT.

Improves Early Build Genome Assemblies using Strand-Seq Data

Bioconductor version: 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

Need some help? Ask on the Bioconductor Support site!

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

System Requirements

URL

Suggests BiocStyle

Linking To Rcpp, BH

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

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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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