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This is the development version of BiocFHIR; for the stable release version, see BiocFHIR.

Illustration of FHIR ingestion and transformation using R

Bioconductor version: Development (3.20)

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.

Author: Vincent Carey [aut, cre]

Maintainer: Vincent Carey <stvjc at>

Citation (from within R, enter citation("BiocFHIR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

BiocFHIR -- infrastructure for parsing and analyzing FHIR data HTML R Script
Handling FHIR documents with BiocFHIR HTML R Script
Linking information between FHIR resources HTML R Script
Transforming FHIR documents to tables with BiocFHIR HTML R Script
Upper level FHIR concepts HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, Infrastructure, Software
Version 1.7.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2)
Imports DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils, methods, BiocBaseUtils
System Requirements
Bug Reports
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Suggests knitr, testthat, rjsoncons, igraph, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package BiocFHIR_1.7.0.tar.gz
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macOS Binary (x86_64) BiocFHIR_1.7.0.tgz
macOS Binary (arm64) BiocFHIR_1.7.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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