Package Recipe 'bioconductor-biocfhir'

recipe bioconductor-biocfhir

Illustration of FHIR ingestion and transformation using R

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/BiocFHIR.html
License:: Artistic-2.0
Recipe:: /bioconductor-biocfhir/meta.yaml

FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. 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¶

Versions:

1.12.0-0, 1.8.0-0, 1.4.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-biocbaseutils >=1.12.0,<1.13.0
on bioconductor-graph >=1.88.0,<1.89.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-dt
on r-jsonlite
on r-shiny
on r-tidyr
on r-visnetwork

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-biocfhir

to add into an existing workspace instead, run:

pixi add bioconductor-biocfhir

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-biocfhir

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-biocfhir

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-biocfhir:<tag>

(see bioconductor-biocfhir/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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-biocfhir/README.html)