recipe bioconductor-biocfhir

Illustration of FHIR ingestion and transformation using R






FHIR R4 bundles in JSON format are derived from Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.

package bioconductor-biocfhir

(downloads) docker_bioconductor-biocfhir



depends bioconductor-biocbaseutils:


depends bioconductor-graph:


depends r-base:


depends r-dplyr:

depends r-dt:

depends r-jsonlite:

depends r-shiny:

depends r-tidyr:

depends r-visnetwork:



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-biocfhir

and update with::

   mamba update bioconductor-biocfhir

To create a new environment, run:

mamba create --name myenvname bioconductor-biocfhir

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-biocfhir/tags`_ for valid values for ``<tag>``)

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