recipe bioconductor-tximeta

Transcript Quantification Import with Automatic Metadata

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/tximeta.html

License:

GPL-2

Recipe:

/bioconductor-tximeta/meta.yaml

Transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.

package bioconductor-tximeta

versions:

1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.4-0,  1.8.0-0,  1.6.3-0,  1.6.2-0, 

1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.4-0,  1.8.0-0,  1.6.3-0,  1.6.2-0,  1.4.3-0,  1.4.0-0,  1.2.2-0,  1.0.3-0,  1.0.1-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-annotationhub:

>=3.8.0,<3.9.0

depends bioconductor-biocfilecache:

>=2.8.0,<2.9.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-ensembldb:

>=2.24.0,<2.25.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends bioconductor-tximport:

>=1.28.0,<1.29.0

depends r-base:

>=4.3,<4.4.0a0

depends r-jsonlite:

depends r-matrix:

depends r-tibble:

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-tximeta

and update with::

   mamba update bioconductor-tximeta

To create a new environment, run:

mamba create --name myenvname bioconductor-tximeta

with myenvname being 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-tximeta:<tag>

(see `bioconductor-tximeta/tags`_ for valid values for ``<tag>``)

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