- recipe bioconductor-bambu
Context-Aware Transcript Quantification from Long Read RNA-Seq data
- Homepage:
- License:
GPL-3 + file LICENSE
- Recipe:
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:
3.4.0-1,3.4.0-0,3.2.4-0,3.0.8-1,3.0.8-0,3.0.6-0,3.0.5-0,3.0.1-0,2.0.6-1,3.4.0-1,3.4.0-0,3.2.4-0,3.0.8-1,3.0.8-0,3.0.6-0,3.0.5-0,3.0.1-0,2.0.6-1,2.0.6-0,2.0.5-0,2.0.3-0,2.0.0-0,1.2.0-0,1.0.2-1,1.0.2-0,1.0.0-2- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-bsgenome:
>=1.70.0,<1.71.0- depends bioconductor-bsgenome:
>=1.70.1,<1.71.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0a0- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0- depends bioconductor-genomicfeatures:
>=1.54.1,<1.55.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx:
>=12- depends r-base:
>=4.3,<4.4.0a0- depends r-data.table:
- depends r-dplyr:
- depends r-rcpp:
- depends r-rcpparmadillo:
- depends r-tidyr:
- depends r-xgboost:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-bambu and update with:: mamba update bioconductor-bambu
To create a new environment, run:
mamba create --name myenvname bioconductor-bambu
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, 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:
[](http://bioconda.github.io/recipes/bioconductor-bambu/README.html)
