recipe bioconductor-flames

FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data



GPL (>= 2)



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.

package bioconductor-flames

(downloads) docker_bioconductor-flames



depends bioconductor-bambu:


depends bioconductor-basilisk:


depends bioconductor-biocgenerics:


depends bioconductor-biostrings:


depends bioconductor-complexheatmap:


depends bioconductor-dropletutils:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicfeatures:


depends bioconductor-genomicranges:


depends bioconductor-ggbio:


depends bioconductor-multiassayexperiment:


depends bioconductor-rhtslib:


depends bioconductor-rsamtools:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends bioconductor-scater:


depends bioconductor-scran:


depends bioconductor-scuttle:


depends bioconductor-singlecellexperiment:


depends bioconductor-summarizedexperiment:


depends bioconductor-zlibbioc:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-circlize:

depends r-cowplot:

depends r-dplyr:

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:



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-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<tag>

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

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