https://github.com/ineelhere/clintrialx
R package to fetch and explore clinical trials data from freely available registries. Fetch data in bulk, customize data and build comprehensive html reports. Currently, it supports the ClinicalTrials.gov registry and CTTI AACT (Access to Aggregate Content of ClinicalTrials.gov).
https://github.com/ineelhere/clintrialx
aact bioinformatics clinical-data clinical-trials clinicaltrialsgov ctti data data-management medical-informatics r-language r-package trials
Last synced: 8 months ago
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R package to fetch and explore clinical trials data from freely available registries. Fetch data in bulk, customize data and build comprehensive html reports. Currently, it supports the ClinicalTrials.gov registry and CTTI AACT (Access to Aggregate Content of ClinicalTrials.gov).
- Host: GitHub
- URL: https://github.com/ineelhere/clintrialx
- Owner: ineelhere
- License: apache-2.0
- Created: 2024-07-18T13:29:15.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-08-28T16:04:20.000Z (about 1 year ago)
- Last Synced: 2024-08-28T17:47:52.627Z (about 1 year ago)
- Topics: aact, bioinformatics, clinical-data, clinical-trials, clinicaltrialsgov, ctti, data, data-management, medical-informatics, r-language, r-package, trials
- Language: R
- Homepage: https://ineelhere.github.io/clintrialx/
- Size: 9.16 MB
- Stars: 12
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
---
output: github_document
editor_options:
markdown:
wrap: 72
---
```{r include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# `ClinTrialX`
[](https://github.com/ineelhere/clintrialx/actions/workflows/R-CMD-check.yaml)
[](https://opensource.org/license/apache-2-0)
[](https://www.indraneelchakraborty.com/clintrialx/)
[](https://github.com/ineelhere/clintrialx)
[](https://CRAN.R-project.org/package=clintrialx)
[](https://CRAN.R-project.org/package=clintrialx)
[](https://clinicaltrials.gov/data-api/api)
[](https://aact.ctti-clinicaltrials.org/)
The goal of `{clintrialx}` is to fetch clinical trials data from freely
available registries. Currently, it supports querying the
- [ClinicalTrials.gov](https://clinicaltrials.gov/) registry using its
[V2 API](https://clinicaltrials.gov/data-api/api) and
- [CTTI AACT](https://aact.ctti-clinicaltrials.org/) (Public Access to
Aggregate Content of ClinicalTrials.gov).
## Installation
Install the package from [CRAN](https://CRAN.R-project.org/package=clintrialx) with:
```r
install.packages("clintrialx")
```
You can install this package from
[GitHub](https://github.com/ineelhere/clintrialx) with:
*you'll need the `devtools` package for this*
``` r
# install.packages("devtools")
devtools::install_github("ineelhere/clintrialx")
```
### Check installation
``` r
library(clintrialx)
```
## Setup AACT account
#### `Only if you wish to use AACT as a source for the data`
- Visit
- Sign up and create an account. It's free.
- The `username` and `password` will be needed to fetch data using
this package.
- Save it in a `.Renviron` file, for example-
``` r
user = "random_name"
password = "random_password"
```
- Now that the file is created, load the variable with the command
`readRenviron("path/to/.Renviron)`
- You're all set!
## Query the [ClinicalTrials.gov](https://clinicaltrials.gov/) Registry
#### Based on NCT IDs
Fetch one or multiple trial records based on NCT IDs. You can opt to
fetch some specific fields or all fields available at source (default).
```{r example1, eval = FALSE}
library(clintrialx)
ctg_get_nct(c("NCT02967965", "NCT04000165", "NCT01007279", "NCT02376244", "NCT01179776"),
fields = c("NCT Number", "Study Title", "Study Status", "Sponsor"))
```
#### Based on fileds
Supports filtering by condition, location, title keywords, intervention,
and overall status.
```{r example2, eval = FALSE}
ctg_get_fields(
condition = "Cancer",
location = "Kolkata",
title = NULL,
intervention = "Drug",
status = c("ACTIVE_NOT_RECRUITING", "RECRUITING"),
page_size = 10
)
```
#### Based on fields - Bulk download
Download all available data for your query. No limits!
*Supports filtering by condition, location, title keywords,
intervention, and overall status.*
```{r example5, eval = FALSE}
df <- ctg_bulk_fetch(location="india")
```
## Query the [CTTI AACT](https://aact.ctti-clinicaltrials.org/)
#### Run Custom Queries
```{r example4, eval = FALSE}
# Set environment variables for database credentials in .Renviron and load it
# readRenviron(".Renviron")
# Connect to the database
con <- aact_connection(Sys.getenv('user'), Sys.getenv('password'))
# Run a custom query
query <- "SELECT nct_id, source, enrollment, overall_status FROM studies LIMIT 5;"
results <- aact_custom_query(con, query)
# Print the results
print(results)
```
## Trial Data HTML Reports
*Currently works for data from ClinicalTrials.Gov*
Visit here for an exqample report -
```{r example6, eval = FALSE}
#first get the data in a R dataframe
my_clinical_trial_data <- ctg_bulk_fetch(condition="cancer")
#now pass it to the reports function
ctg_data_report(
ctg_data = my_clinical_trial_data,
title = "Clinical Trials Analysis",
author = "Indra",
output_file = "reports/clinical_trials.html",
theme = "flatly",
color_palette = c("#4E79A7", "#F28E2B", "#E15759", "#76B7B2", "#59A14F", "#EDC948"),
include_data_quality = TRUE,
include_interactive_plots = TRUE,
custom_footer = "Proprietary report generated by SomeGreatOrg Inc."
)
# Generate a report with static plots and no data quality assessment
ctg_data_report(
ctg_data = my_clinical_trial_data,
title = "Quick Clinical Trial Overview",
include_data_quality = FALSE,
include_interactive_plots = FALSE
)
```
Check the path `reports/clinical_trials.html` on your local. It will
have the html report file.
Cool stuff - It also has the codes to the plots!
## Data Sources
You can fetch version information directly from the package:
```{r example3, eval = FALSE}
version_info(source = "clinicaltrials.gov")
```
## Get Involved
🚀 Ready to contribute? Let's make clintrialx even better!
- Fork the [GitHub](https://github.com/ineelhere/clintrialx) repo.
- Check out your development branch from the dev branch.
- Do your work on a feature (ftr) branch.
- Raise a PR against the dev branch of the [clintrialx](https://github.com/ineelhere/clintrialx) repo.
- Sit back and [relax](https://www.youtube.com/watch?v=Uffjii1hXzU) while I review it!
💬 **Questions or Feedback?** Feel free to open an issue on [GitHub
Issues page](https://github.com/ineelhere/clintrialx/issues).
🌟 **Enjoying `clintrialx`?** Please consider giving it a star on
[GitHub](https://github.com/ineelhere/clintrialx)! Your support helps
this project grow and improve.
More updates to come. Happy coding! 🎉