Package Recipe 'bioconductor-bambu'

recipe bioconductor-bambu

Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

Homepage:: https://bioconductor.org/packages/3.14/bioc/html/bambu.html
License:: GPL-3 + file LICENSE
Recipe:: /bioconductor-bambu/meta.yaml

bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.

package bioconductor-bambu¶

Versions:

2.0.6-1, 2.0.6-0, 2.0.5-0, 2.0.3-0, 2.0.0-0, 1.2.0-0, 1.0.2-1, 1.0.2-0, 1.0.0-2

Depends:

bioconductor-biocgenerics >=0.40.0,<0.41.0
bioconductor-biocparallel >=1.28.0,<1.29.0
bioconductor-bsgenome >=1.62.0,<1.63.0
bioconductor-genomeinfodb >=1.30.0,<1.31.0
bioconductor-genomicalignments >=1.30.0,<1.31.0
bioconductor-genomicfeatures >=1.46.0,<1.47.0
bioconductor-genomicranges >=1.46.0,<1.47.0
bioconductor-iranges >=2.28.0,<2.29.0
bioconductor-rsamtools >=2.10.0,<2.11.0
bioconductor-s4vectors >=0.32.0,<0.33.0
bioconductor-summarizedexperiment >=1.24.0,<1.25.0
libblas >=3.9.0,<4.0a0
libgcc-ng >=12
liblapack >=3.9.0,<4.0a0
libstdcxx-ng >=12
r-base >=4.1,<4.2.0a0
r-data.table
r-dplyr
r-rcpp
r-rcpparmadillo
r-tidyr
r-xgboost

Required By:

Installation

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

conda install bioconductor-bambu

and update with:

conda update bioconductor-bambu

or use the docker container:

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

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

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-bambu/README.html)