recipe spanki

Spanki is a set of tools to facilitate analysis of alternative splicing from RNA-Seq data. Spanki compiles quantitative and qualitative information about junction alignments from input BAM files, and analyzes junction-level splicing along with pairwise-defined splicing events. A simulator is also included to evaluate junction detection performance.






package spanki

(downloads) docker_spanki



depends biopython:

depends cufflinks:

depends fisher:

depends numpy:

depends pyfasta:

depends pysam:

depends python:


depends samtools:

depends statsmodels:



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 spanki

and update with::

   mamba update spanki

To create a new environment, run:

mamba create --name myenvname spanki

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 `spanki/tags`_ for valid values for ``<tag>``)

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