:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-pram' .. highlight: bash bioconductor-pram ================= .. conda:recipe:: bioconductor-pram :replaces_section_title: :noindex: Pooling RNA\-seq datasets for assembling transcript models :homepage: https://bioconductor.org/packages/3.18/bioc/html/pram.html :license: GPL (>= 3) :recipe: /`bioconductor-pram `_/`meta.yaml `_ Publicly available RNA\-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA\-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA\-seq datasets\, we developed a new R package named Pooling RNA\-seq and Assembling Models \(PRAM\)\, which builds transcript models in intergenic regions from pooled RNA\-seq datasets. This package includes functions for defining intergenic regions\, extracting and pooling related RNA\-seq alignments\, predicting\, selected\, and evaluating transcript models. .. conda:package:: bioconductor-pram |downloads_bioconductor-pram| |docker_bioconductor-pram| :versions: .. raw:: html
1.18.0-01.16.0-01.14.0-01.10.0-01.8.0-01.6.0-11.6.0-01.4.0-01.2.0-0 ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1`` .. raw:: html
:depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-data.table: ``>=1.11.8`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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-pram and update with:: mamba update bioconductor-pram To create a new environment, run:: mamba create --name myenvname bioconductor-pram 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-pram: (see `bioconductor-pram/tags`_ for valid values for ````) .. |downloads_bioconductor-pram| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-pram.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-pram :alt: (downloads) .. |docker_bioconductor-pram| image:: https://quay.io/repository/biocontainers/bioconductor-pram/status :target: https://quay.io/repository/biocontainers/bioconductor-pram .. _`bioconductor-pram/tags`: https://quay.io/repository/biocontainers/bioconductor-pram?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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-pram/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-pram/README.html