recipe bioconductor-contibait

Improves Early Build Genome Assemblies using Strand-Seq Data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/contiBAIT.html

License:

BSD_2_clause + file LICENSE

Recipe:

/bioconductor-contibait/meta.yaml

Links:

biotools: contibait, doi: 10.1093/bioinformatics/btx281

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.

package bioconductor-contibait

Versions:

1.26.0-1,  1.26.0-0,  1.22.0-2,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.15.0-0, 

1.26.0-1,  1.26.0-0,  1.22.0-2,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.15.0-0,  1.14.0-0,  1.12.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-dnacopy >=1.72.0,<1.73.0

• bioconductor-exomecopy >=1.44.0,<1.45.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicfiles >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-bh >=1.51.0.3

• r-clue

• r-cluster

• r-colorspace

• r-data.table

• r-diagram

• r-ggplot2

• r-gplots

• r-gtools

• r-rcpp

• r-reshape2

• r-tsp

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-contibait

and update with:

conda update bioconductor-contibait

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-contibait:<tag>

(see bioconductor-contibait/tags for valid values for <tag>)

Download stats

Link to this page

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