contiBAIT
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see contiBAIT.
Improves Early Build Genome Assemblies using Strand-Seq Data
Bioconductor version: Release (3.19)
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("contiBAIT")):
Installation
To install this package, start R (version "4.4") 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
| Reference Manual |
Details
| biocViews | CellBasedAssays, Genetics, GenomeAssembly, ImmunoOncology, QualityControl, Software, WholeGenome |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/contiBAIT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/contiBAIT |
| Package Short Url | https://bioconductor.org/packages/contiBAIT/ |
| Package Downloads Report | Download Stats |