recipe bioconductor-bambu

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Homepage:

https://bioconductor.org/packages/3.16/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:

3.0.6-0,  3.0.5-0,  3.0.1-0,  2.0.6-1,  2.0.6-0,  2.0.5-0,  2.0.3-0,  2.0.0-0,  1.2.0-0, 

3.0.6-0,  3.0.5-0,  3.0.1-0,  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 >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• 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-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• 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-data.table

• r-dplyr

• r-rcpp

• r-rcpparmadillo

• r-tidyr

• r-xgboost

Required By:

• bioconductor-flames

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>)

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