contiBAIT
Improves Early Build Genome Assemblies using Strand-Seq Data
Bioconductor version: Release (3.17)
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 | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, Genetics, GenomeAssembly, ImmunoOncology, QualityControl, Software, WholeGenome |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (7.5 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 |
| Linking To | Rcpp, BH |
| Suggests | BiocStyle |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | contiBAIT_1.28.0.tar.gz |
| Windows Binary | contiBAIT_1.28.0.zip |
| macOS Binary (x86_64) | contiBAIT_1.28.0.tgz |
| macOS Binary (arm64) | contiBAIT_1.28.0.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 |