:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-flames' .. highlight: bash bioconductor-flames =================== .. conda:recipe:: bioconductor-flames :replaces_section_title: :noindex: FLAMES\: Full Length Analysis of Mutations and Splicing in long read RNA\-seq data :homepage: https://bioconductor.org/packages/3.18/bioc/html/FLAMES.html :license: GPL (>= 2) :recipe: /`bioconductor-flames `_/`meta.yaml `_ Semi\-supervised isoform detection and annotation from both bulk and single\-cell long read RNA\-seq data. Flames provides automated pipelines for analysing isoforms\, as well as intermediate functions for manual execution. .. conda:package:: bioconductor-flames |downloads_bioconductor-flames| |docker_bioconductor-flames| :versions: ``1.8.0-0``,  ``1.6.0-0``,  ``1.3.4-1``,  ``1.3.4-0``,  ``1.0.2-2``,  ``1.0.2-1``,  ``1.0.2-0``,  ``0.99.31-0`` :depends bioconductor-bambu: ``>=3.4.0,<3.5.0`` :depends bioconductor-bambu: ``>=3.4.0,<3.5.0a0`` :depends bioconductor-basilisk: ``>=1.14.0,<1.15.0`` :depends bioconductor-basilisk: ``>=1.14.1,<1.15.0a0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-biostrings: ``>=2.70.1,<2.71.0a0`` :depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0`` :depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0a0`` :depends bioconductor-dropletutils: ``>=1.22.0,<1.23.0`` :depends bioconductor-dropletutils: ``>=1.22.0,<1.23.0a0`` :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-ggbio: ``>=1.50.0,<1.51.0`` :depends bioconductor-ggbio: ``>=1.50.0,<1.51.0a0`` :depends bioconductor-multiassayexperiment: ``>=1.28.0,<1.29.0`` :depends bioconductor-multiassayexperiment: ``>=1.28.0,<1.29.0a0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0a0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0a0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0a0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0`` :depends bioconductor-scater: ``>=1.30.0,<1.31.0`` :depends bioconductor-scater: ``>=1.30.1,<1.31.0a0`` :depends bioconductor-scran: ``>=1.30.0,<1.31.0`` :depends bioconductor-scran: ``>=1.30.0,<1.31.0a0`` :depends bioconductor-scuttle: ``>=1.12.0,<1.13.0`` :depends bioconductor-scuttle: ``>=1.12.0,<1.13.0a0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0a0`` :depends bioconductor-zlibbioc: ``>=1.48.0,<1.49.0`` :depends bioconductor-zlibbioc: ``>=1.48.0,<1.49.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends libstdcxx-ng: ``>=12`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-circlize: :depends r-cowplot: :depends r-dplyr: :depends r-future: :depends r-ggplot2: :depends r-gridextra: :depends r-igraph: :depends r-jsonlite: :depends r-magrittr: :depends r-matrix: :depends r-rcolorbrewer: :depends r-rcpp: :depends r-reticulate: :depends r-stringr: :depends r-tidyr: :depends r-withr: :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-flames and update with:: mamba update bioconductor-flames To create a new environment, run:: mamba create --name myenvname bioconductor-flames 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-flames: (see `bioconductor-flames/tags`_ for valid values for ````) .. |downloads_bioconductor-flames| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-flames.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-flames :alt: (downloads) .. |docker_bioconductor-flames| image:: https://quay.io/repository/biocontainers/bioconductor-flames/status :target: https://quay.io/repository/biocontainers/bioconductor-flames .. _`bioconductor-flames/tags`: https://quay.io/repository/biocontainers/bioconductor-flames?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-flames/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-flames/README.html