BiocFHIR
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 (3.24)
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.
Author: Vincent Carey [aut, cre]
Maintainer: Vincent Carey <stvjc at channing.harvard.edu>
citation("BiocFHIR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("BiocFHIR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BiocFHIR")| 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Software |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2) |
| Imports | DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils, methods, BiocBaseUtils |
| System Requirements | |
| URL | https://github.com/vjcitn/BiocFHIR |
| Bug Reports | https://github.com/vjcitn/BiocFHIR/issues |
See More
| Suggests | knitr, testthat, rjsoncons, igraph, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BiocFHIR_1.15.0.tar.gz |
| Windows Binary (x86_64) | BiocFHIR_1.15.0.zip |
| macOS Binary (big-sur-x86_64) | BiocFHIR_1.15.0.tgz |
| macOS Binary (sonoma-arm64) | BiocFHIR_1.15.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BiocFHIR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BiocFHIR |
| Bioc Package Browser | https://code.bioconductor.org/browse/BiocFHIR/ |
| Package Short Url | https://bioconductor.org/packages/BiocFHIR/ |
| Package Downloads Report | Download Stats |