Showing 27 of total 27 results (show query)
insightsengineering
teal:Exploratory Web Apps for Analyzing Clinical Trials Data
A 'shiny' based interactive exploration framework for analyzing clinical trials data. 'teal' currently provides a dynamic filtering facility and different data viewers. 'teal' 'shiny' applications are built using standard 'shiny' modules.
Maintained by Dawid Kaledkowski. Last updated 1 months ago.
clinical-trialsnestshinywebapp
206 stars 12.65 score 176 scripts 5 dependents
ropensci
RNeXML:Semantically Rich I/O for the 'NeXML' Format
Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
Maintained by Carl Boettiger. Last updated 11 months ago.
metadatanexmlphylogeneticslinked-data
13 stars 9.97 score 100 scripts 19 dependents
atorus-research
Tplyr:A Traceability Focused Grammar of Clinical Data Summary
A traceability focused tool created to simplify the data manipulation necessary to create clinical summaries.
Maintained by Mike Stackhouse. Last updated 1 years ago.
95 stars 9.49 score 138 scripts 2 dependents
ramiromagno
gwasrapidd:'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog
'GWAS' R 'API' Data Download. This package provides easy access to the 'NHGRI'-'EBI' 'GWAS' Catalog data by accessing the 'REST' 'API' <https://www.ebi.ac.uk/gwas/rest/docs/api/>.
Maintained by Ramiro Magno. Last updated 1 years ago.
thirdpartyclientbiomedicalinformaticsgenomewideassociationsnpassociation-studiesgwas-cataloghumanrest-clienttraittrait-ontology
95 stars 8.10 score 49 scripts 1 dependents
edubruell
tidyllm:Tidy Integration of Large Language Models
A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'Openai', 'Gemini','Mistral' and local models via 'Ollama' into R workflows. The package supports text and media-based interactions, interactive message history, batch request APIs, and a tidy, pipeline-oriented interface for streamlined integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://aistudio.google.com/>, <https://mistral.ai/> and <https://ollama.com>.
Maintained by Eduard Brüll. Last updated 2 days ago.
70 stars 7.87 score 26 scripts
mrc-ide
naomi:Naomi Model for Subnational HIV Estimates
This package implements the Naomi model for subnational HIV estimates.
Maintained by Jeff Eaton. Last updated 20 days ago.
9 stars 7.74 score 54 scripts 2 dependents
wincowgerdev
OpenSpecy:Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples (Cowger et al. 2021, <doi:10.1021/acs.analchem.1c00123>). With read_any(), Open Specy provides a single function for reading individual, batch, or map spectral data files like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies processing spectra, including smoothing, baseline correction, range restriction and flattening, intensity conversions, wavenumber alignment, and min-max normalization. Spectra can be identified in batch using an onboard reference library (Cowger et al. 2020, <doi:10.1177/0003702820929064>) using match_spec(). A Shiny app is available via run_app() or online at <https://openanalysis.org/openspecy/>.
Maintained by Win Cowger. Last updated 30 days ago.
29 stars 7.55 score 22 scripts
bioc
CuratedAtlasQueryR:Queries the Human Cell Atlas
Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object.
Maintained by Stefano Mangiola. Last updated 5 months ago.
assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomicsdatabaseduckdbhdf5human-cell-atlassingle-cellsinglecellexperimenttidyverse
90 stars 7.04 score 41 scripts
usaid-oha-si
gophr:Utility functions related to working with the MER Structured Dataset
This packages contains a number of functions for working with the PEPFAR MSD.
Maintained by Aaron Chafetz. Last updated 5 months ago.
1 stars 6.21 score 182 scripts 1 dependents
justincally
VicmapR:Access Victorian Spatial Data Through Web File Services (WFS)
Easily interfaces R to spatial datasets available through the Victorian Government's WFS (Web Feature Service): <https://opendata.maps.vic.gov.au/geoserver/ows?request=GetCapabilities&service=wfs>, which allows users to read in 'sf' data from these sources. VicmapR uses the lazy querying approach and code developed by Teucher et al. (2021) for the 'bcdata' R package <doi:10.21105/joss.02927>.
Maintained by Justin Cally. Last updated 7 months ago.
17 stars 6.14 score 18 scripts
jedick
chem16S:Chemical Metrics for Microbial Communities
Combines taxonomic classifications of high-throughput 16S rRNA gene sequences with reference proteomes of archaeal and bacterial taxa to generate amino acid compositions of community reference proteomes. Calculates chemical metrics including carbon oxidation state ('Zc'), stoichiometric oxidation and hydration state ('nO2' and 'nH2O'), H/C, N/C, O/C, and S/C ratios, grand average of hydropathicity ('GRAVY'), isoelectric point ('pI'), protein length, and average molecular weight of amino acid residues. Uses precomputed reference proteomes for archaea and bacteria derived from the Genome Taxonomy Database ('GTDB'). Also includes reference proteomes derived from the NCBI Reference Sequence ('RefSeq') database and manual mapping from the 'RDP Classifier' training set to 'RefSeq' taxonomy as described by Dick and Tan (2023) <doi:10.1007/s00248-022-01988-9>. Processes taxonomic classifications in 'RDP Classifier' format or OTU tables in 'phyloseq-class' objects from the Bioconductor package 'phyloseq'.
Maintained by Jeffrey Dick. Last updated 9 days ago.
16s-rrnacarbon-oxidation-statechemical-metricsgenomic-adaptationmicrobial-communities
4 stars 5.89 score 8 scripts
lchansson
rKolada:Access Data from the 'Kolada' Database
Methods for downloading and processing data and metadata from 'Kolada', the official Swedish regions and municipalities database <https://www.kolada.se/>.
Maintained by Love Hansson. Last updated 11 months ago.
4 stars 5.30 score 5 scripts
roaldarbol
animovement:An R toolbox for analysing animal movement across space and time
An R toolbox for analysing animal movement across space and time.
Maintained by Mikkel Roald-Arbøl. Last updated 3 months ago.
animal-behaviouranimal-movementneuroethologyneuroscience
10 stars 4.81 score 8 scripts
damurka
khisr:An R Client to Retrieve Data from DHIS2
Provides a user-friendly interface for interacting with the District Health Information Software 2 (DHIS2) instance. It streamlines data retrieval, empowering researchers, analysts, and healthcare professionals to obtain and utilize data efficiently.
Maintained by David Kariuki. Last updated 6 months ago.
1 stars 4.78 score 7 scripts 1 dependents
danielquiroz97
RGCxGC:Preprocessing and Multivariate Analysis of Bidimensional Gas Chromatography Data
Toolbox for chemometrics analysis of bidimensional gas chromatography data. This package import data for common scientific data format (NetCDF) and fold it to 2D chromatogram. Then, it can perform preprocessing and multivariate analysis. In the preprocessing algorithms, baseline correction, smoothing, and peak alignment are available. While in multivariate analysis, multiway principal component analysis is incorporated.
Maintained by Cristian Quiroz-Moreno. Last updated 2 years ago.
chemphyschemometricsgcxgcmultiway-algorithmspreprocessing
7 stars 4.77 score 17 scripts
kof-ch
kofdata:Get Data from the 'KOF Datenservice' API
Read Swiss time series data from the 'KOF Data' API, <https://datenservice.kof.ethz.ch>. The API provides macro economic time series data mostly about Switzerland. The package itself is a set of wrappers around the 'KOF Datenservice' API. The 'kofdata' package is able to consume public information as well as data that requires an API token.
Maintained by Oliver Müller. Last updated 1 years ago.
4 stars 4.57 score 62 scriptsbioc
ribor:An R Interface for Ribo Files
The ribor package provides an R Interface for .ribo files. It provides functionality to read the .ribo file, which is of HDF5 format, and performs common analyses on its contents.
Maintained by Michael Geng. Last updated 5 months ago.
4.51 score 32 scripts
pepijn-devries
openmpt:Open 'ModPlug' Tracker Port
Tracker music uses audio samples and pattern tables to organise musical compositions. Such music is stored in module files. This package reads, renders and plays module files using the 'libopenmpt' library <https://lib.openmpt.org/>.
Maintained by Pepijn de Vries. Last updated 2 months ago.
audiomoduleslibopenmptportaudio19cpp
2 stars 4.43 score 7 scripts
pierreroudier
asdreader:Reading ASD Binary Files in R
A simple driver that reads binary data created by the ASD Inc. portable spectrometer instruments, such as the FieldSpec (for more information, see <http://www.asdi.com/products/fieldspec-spectroradiometers>). Spectral data can be extracted from the ASD files as raw (DN), white reference, radiance, or reflectance. Additionally, the metadata information contained in the ASD file header can also be accessed.
Maintained by Pierre Roudier. Last updated 8 years ago.
11 stars 4.04 score 9 scripts
josesamos
geogenr:Generator from American Community Survey Geodatabases
The American Community Survey (ACS) <https://www.census.gov/programs-surveys/acs> offers geodatabases with geographic information and associated data of interest to researchers in the area. The goal of this package is to generate objects that allow us to access and consult the information available in various formats, such as in 'GeoPackage' format or in multidimensional 'ROLAP' (Relational On-Line Analytical Processing) star format.
Maintained by Jose Samos. Last updated 11 months ago.
2 stars 4.00 score 8 scripts
sumtxt
bonn:Access INKAR Database
Retrieve and import data from the INKAR database (Indikatoren und Karten zur Raum- und Stadtentwicklung Datenbank, <[https://www.inkar.de]https://www.inkar.de>) of the Federal Office for Building and Regional Planning (BBSR) in Bonn using their JSON API.
Maintained by Moritz Marbach. Last updated 2 years ago.
17 stars 3.93 score 3 scripts
sammorrissette
SC2API:Blizzard SC2 API Wrapper
A wrapper for Blizzard's Starcraft II (a 2010 real-time strategy game) Application Programming Interface (API). All documented API calls are implemented in an easy-to-use and consistent manner.
Maintained by Samuel Morrissette. Last updated 5 years ago.
1 stars 3.70 score 4 scripts
gleon
laketemps:Lake Temperatures Collected by Situ and Satellite Methods from 1985-2009
Lake temperature records, metadata, and climate drivers for 291 global lakes during the time period 1985-2009. Temperature observations were collected using satellite and in situ methods. Climatic drivers and geomorphometric characteristics were also compiled and are included for each lake. Data are part of the associated publication from the Global Lake Temperature Collaboration project (http://www.laketemperature.org). See citation('laketemps') for dataset attribution.
Maintained by Jordan S Read. Last updated 8 years ago.
2 stars 3.04 score 11 scripts
luomus
f2g:FinBIF to GBIF
Tools for publishing FinBIF data to GBIF.
Maintained by William K. Morris. Last updated 6 days ago.
1 stars 3.02 score
ropengov
kelaopendata:Access open data from National social insurance institution of Finland
Designed to simplify and speed up access to open data from National social insurance institution of Finland (KELA) published at <https://www.avoindata.fi/data/fi/organization/kela>, the kelaopendata package offers researchers and analysts a set of tools to obtain data and metadata for a wide range of applications.
Maintained by Markus Kainu. Last updated 4 months ago.
dataopen-datasocial-security-data
1 stars 2.40 score
cran
OnboardClient:Bindings for Onboard Data's Building Data API
Provides a wrapper for the Onboard Data building data API <https://api.onboarddata.io/swagger>. Along with streamlining access to the API, this package simplifies access to sensor time series data, metadata (sensors, equipment, and buildings), and details about the Onboard data model/ontology.
Maintained by Christopher Dudas-Thomas. Last updated 2 years ago.
1.00 score