Showing 71 of total 71 results (show query)
luomus
finbif:Interface for the 'Finnish Biodiversity Information Facility' API
A programmatic interface to the 'Finnish Biodiversity Information Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates Finnish biodiversity data from multiple sources in a single open access portal for researchers, citizen scientists, industry and government. 'FinBIF' allows users of biodiversity information to find, access, combine and visualise data on Finnish plants, animals and microorganisms. The 'finbif' package makes the publicly available data in 'FinBIF' easily accessible to programmers. Biodiversity information is available on taxonomy and taxon occurrence. Occurrence data can be filtered by taxon, time, location and other variables. The data accessed are conveniently preformatted for subsequent analyses.
Maintained by William K. Morris. Last updated 6 days ago.
apibiodiversitybiodiversity-informaticsbiodiversity-informationfinbiffinbif-accessoccurrencesr-programmingspeciesspecimenstaxontaxonomyweb-services
7.5 match 5 stars 8.15 score 42 scripts 3 dependents
funecology
fundiversity:Easy Computation of Functional Diversity Indices
Computes six functional diversity indices. These are namely, Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic), Functional Richness intersections (FRic_intersect), Functional Dispersion (FDis), and Rao's entropy (Q) (reviewed in Villéger et al. 2008 <doi:10.1890/07-1206.1>). Provides efficient, modular, and parallel functions to compute functional diversity indices (Grenié & Gruson 2023 <doi:10.1111/ecog.06585>).
Maintained by Matthias Grenié. Last updated 8 months ago.
biodiversitybiodiversity-indicatorsbiodiversity-informaticsfunctional-diversityfunctional-ecologyfunctional-traitfunctional-traitstraittrait-basedtraits
7.5 match 38 stars 7.34 score 38 scripts
ropensci
occCite:Querying and Managing Large Biodiversity Occurrence Datasets
Facilitates the gathering of biodiversity occurrence data from disparate sources. Metadata is managed throughout the process to facilitate reporting and enhanced ability to repeat analyses.
Maintained by Hannah L. Owens. Last updated 5 months ago.
biodiversity-databiodiversity-informaticsbiodiversity-standardscitationsmuseum-collection-specimensmuseum-collectionsmuseum-metadata
7.5 match 23 stars 7.30 score 43 scripts
biogeomacro
GIFT:Access to the Global Inventory of Floras and Traits (GIFT)
Retrieving regional plant checklists, species traits and distributions, and environmental data from the Global Inventory of Floras and Traits (GIFT). More information about the GIFT database can be found at <https://gift.uni-goettingen.de/about> and the map of available floras can be visualized at <https://gift.uni-goettingen.de/map>. The API and associated queries can be accessed according the following scheme: <https://gift.uni-goettingen.de/api/extended/index2.0.php?query=env_raster>.
Maintained by Pierre Denelle. Last updated 6 days ago.
biodiversitybiodiversity-informaticsplants-databaseplants-distribution
7.5 match 18 stars 6.51 score 24 scripts
adrientaudiere
MiscMetabar:Miscellaneous Functions for Metabarcoding Analysis
Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
Maintained by Adrien Taudière. Last updated 26 days ago.
sequencingmicrobiomemetagenomicsclusteringclassificationvisualizationampliconamplicon-sequencingbiodiversity-informaticsecologyilluminametabarcodingngs-analysis
7.5 match 17 stars 6.44 score 23 scripts
bioc
Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.
Maintained by Nan Xiao. Last updated 5 months ago.
softwaredataimportdatarepresentationfeatureextractioncheminformaticsbiomedicalinformaticsproteomicsgosystemsbiologybioconductorbioinformaticsdrug-discoveryfeature-extractionfingerprintmolecular-descriptorsprotein-sequences
6.1 match 37 stars 7.81 score 29 scripts
hms-dbmi
EHRtemporalVariability:Delineating Temporal Dataset Shifts in Electronic Health Records
Functions to delineate temporal dataset shifts in Electronic Health Records through the projection and visualization of dissimilarities among data temporal batches. This is done through the estimation of data statistical distributions over time and their projection in non-parametric statistical manifolds, uncovering the patterns of the data latent temporal variability. 'EHRtemporalVariability' is particularly suitable for multi-modal data and categorical variables with a high number of values, common features of biomedical data where traditional statistical process control or time-series methods may not be appropriate. 'EHRtemporalVariability' allows you to explore and identify dataset shifts through visual analytics formats such as Data Temporal heatmaps and Information Geometric Temporal (IGT) plots. An additional 'EHRtemporalVariability' Shiny app can be used to load and explore the package results and even to allow the use of these functions to those users non-experienced in R coding. (Sáez et al. 2020) <doi:10.1093/gigascience/giaa079>.
Maintained by Carlos Sáez. Last updated 11 months ago.
biomedical-data-sciencebiomedical-informaticsdata-qualitydata-quality-monitoringdataset-shiftselectronic-health-recordstimevariabilityvisualization
9.0 match 17 stars 5.27 score 22 scripts
ngiangre
kidsides:Download, Cache, and Connect to 'KidSIDES'
Caches and then connects to a 'sqlite' database containing half a million pediatric drug safety signals. The database is part of a family of resources catalogued at <https://nsides.io>. The database contains 17 tables where the description table provides a map between the fields the field's details. The database was created by Nicholas Giangreco during his PhD thesis which you can read in Giangreco (2022) <doi:10.7916/d8-5d9b-6738>. The observations are from the Food and Drug Administration's Adverse Event Reporting System. Generalized additive models estimated drug effects across child development stages for the occurrence of an adverse event when exposed to a drug compared to other drugs. Read more at the methods detailed in Giangreco (2022) <doi:10.1016/j.medj.2022.06.001>.
Maintained by Nicholas Giangreco. Last updated 2 years ago.
databasedruggeneralized-additive-modelsinformaticspediatricspharmacovigilancepkgdownsafety
10.0 match 5 stars 4.40 score 5 scripts
ineelhere
clintrialx:Connect and Work with Clinical Trials Data Sources
Are you spending too much time fetching and managing clinical trial data? Struggling with complex queries and bulk data extraction? What if you could simplify this process with just a few lines of code? Introducing 'clintrialx' - Fetch clinical trial data from sources like 'ClinicalTrials.gov' <https://clinicaltrials.gov/> and the 'Clinical Trials Transformation Initiative - Access to Aggregate Content of ClinicalTrials.gov' database <https://aact.ctti-clinicaltrials.org/>, supporting pagination and bulk downloads. Also, you can generate HTML reports based on the data obtained from the sources!
Maintained by Indraneel Chakraborty. Last updated 5 days ago.
aactbioinformaticsclinical-dataclinical-trialsclinicaltrialsgovcttidatadata-managementmedical-informaticsr-languagetrials
7.5 match 15 stars 5.76 score 11 scripts
shaunpwilkinson
insect:Informatic Sequence Classification Trees
Provides tools for probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018) <doi:10.7287/peerj.preprints.26812v1>.
Maintained by Shaun Wilkinson. Last updated 4 years ago.
7.3 match 14 stars 5.80 score 91 scripts
bhklab
CREAM:Clustering of Genomic Regions Analysis Method
Provides a new method for identification of clusters of genomic regions within chromosomes. Primarily, it is used for calling clusters of cis-regulatory elements (COREs). 'CREAM' uses genome-wide maps of genomic regions in the tissue or cell type of interest, such as those generated from chromatin-based assays including DNaseI, ATAC or ChIP-Seq. 'CREAM' considers proximity of the elements within chromosomes of a given sample to identify COREs in the following steps: 1) It identifies window size or the maximum allowed distance between the elements within each CORE, 2) It identifies number of elements which should be clustered as a CORE, 3) It calls COREs, 4) It filters the COREs with lowest order which does not pass the threshold considered in the approach.
Maintained by Benjamin Haibe-Kains. Last updated 4 years ago.
peakdetectionfunctionalpredictionbiomedicalinformaticsclusteringbiomedical-informaticsfunctional-predictionpeak-detection
7.5 match 12 stars 5.43 score 15 scripts
johnmackintosh
cusumcharter:Easier CUSUM Control Charts
Create CUSUM (cumulative sum) statistics from a vector or dataframe. Also create single or faceted CUSUM control charts, with or without control limits. Accepts vector, dataframe, tibble or data.table inputs.
Maintained by John MacKintosh. Last updated 4 months ago.
cusumggplot2health-informaticshealthcarequality-improvementrdatatablestatistical-process-control
7.5 match 27 stars 5.13 score 9 scripts
overton-group
eHDPrep:Quality Control and Semantic Enrichment of Datasets
A tool for the preparation and enrichment of health datasets for analysis (Toner et al. (2023) <doi:10.1093/gigascience/giad030>). Provides functionality for assessing data quality and for improving the reliability and machine interpretability of a dataset. 'eHDPrep' also enables semantic enrichment of a dataset where metavariables are discovered from the relationships between input variables determined from user-provided ontologies.
Maintained by Ian Overton. Last updated 2 years ago.
data-qualityhealth-informaticssemantic-enrichment
7.5 match 8 stars 4.90 score 10 scripts
b-cubed-eu
gcube:Simulating Biodiversity Data Cubes
This R package provides a simulation framework for biodiversity data cubes. This can start from simulating multiple species distributed in a landscape over a temporal scope. In a second phase, the simulation of a variety of observation processes and effort can generate actual occurrence datasets. Based on their (simulated) spatial uncertainty, occurrences can then be designated to a grid to form a data cube.
Maintained by Ward Langeraert. Last updated 1 months ago.
biodiversity-informaticsdata-cubessimulations
7.5 match 6 stars 4.60 score 9 scripts
ohdsi
OhdsiReportGenerator:Observational Health Data Sciences and Informatics Report Generator
Extract results into R from the Observational Health Data Sciences and Informatics result database (see <https://ohdsi.github.io/Strategus/results-schema/index.html>) and generate reports/presentations via 'quarto' that summarize results in HTML format. Learn more about 'OhdsiReportGenerator' at <https://ohdsi.github.io/OhdsiReportGenerator/>.
Maintained by Jenna Reps. Last updated 18 days ago.
6.1 match 4.54 score 2 scriptsropensci
ReLTER:An Interface for the eLTER Community
ReLTER provides access to DEIMS-SDR (https://deims.org/), and allows interaction with data and software implemented by eLTER Research Infrastructure (RI) thus improving data sharing among European LTER projects. ReLTER uses the R language to access and interact with the DEIMS-SDR archive of information shared by the Long Term Ecological Research (LTER) network. This package grew within eLTER H2020 as a major project that will help advance the development of European Long-Term Ecosystem Research Infrastructures (eLTER RI - https://elter-ri.eu). The ReLTER package functions in particular allow to: - retrieve the information about entities (e.g. sites, datasets, and activities) shared by DEIMS-SDR (see e.g. get_site_info function); - interact with the [ODSEurope](maps.opendatascience.eu) starting with the dataset shared by [DEIMS-SDR](https://deims.org/) (see e.g. [get_site_ODS](https://docs.ropensci.org/ReLTER/reference/get_site_ODS.html) function); - use the eLTER site informations to download and crop geospatial data from other platforms (see e.g. get_site_ODS function); - improve the quality of the dataset (see e.g. get_id_worms). Functions currently implemented are derived from discussions of the needs among the eLTER users community. The ReLTER package will continue to follow the progress of eLTER-RI and evolve, adding new tools and improvements as required.
Maintained by Alessandro Oggioni. Last updated 1 years ago.
biodiversity-informaticsdata-scienceecologyelterresearch-infrastructure
7.5 match 12 stars 3.38 score 4 scripts
r-spatial
mapview:Interactive Viewing of Spatial Data in R
Quickly and conveniently create interactive visualisations of spatial data with or without background maps. Attributes of displayed features are fully queryable via pop-up windows. Additional functionality includes methods to visualise true- and false-color raster images and bounding boxes.
Maintained by Tim Appelhans. Last updated 3 months ago.
gisleafletmapsspatialvisualizationweb-mapping
1.5 match 525 stars 14.28 score 7.3k scripts 25 dependents
smithsonian
gde:GBIF Dataset Explorer
Functions to explore datasets from the Global Biodiversity Information Facility (GBIF - <https://www.gbif.org/>) using a Shiny interface.
Maintained by Luis J Villanueva. Last updated 2 years ago.
biodiversity-informaticsdata-issuesgbifgbif-dataoccurrenceshinyshiny-r
7.5 match 1 stars 2.70 scoreohdsi
DatabaseConnector:Connecting to Various Database Platforms
An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server', 'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', 'Snowflake', 'Spark', 'SQLite', and 'InterSystems IRIS'). Also includes support for fetching data as 'Andromeda' objects. Uses either 'Java Database Connectivity' ('JDBC') or other 'DBI' drivers to connect to databases.
Maintained by Martijn Schuemie. Last updated 2 months ago.
1.5 match 56 stars 12.63 score 772 scripts 11 dependentsohdsi
PatientLevelPrediction:Develop Clinical Prediction Models Using the Common Data Model
A user friendly way to create patient level prediction models using the Observational Medical Outcomes Partnership Common Data Model. Given a cohort of interest and an outcome of interest, the package can use data in the Common Data Model to build a large set of features. These features can then be used to fit a predictive model with a number of machine learning algorithms. This is further described in Reps (2017) <doi:10.1093/jamia/ocy032>.
Maintained by Egill Fridgeirsson. Last updated 9 days ago.
1.6 match 190 stars 10.85 score 297 scripts
muschellij2
cifti:Toolbox for Connectivity Informatics Technology Initiative ('CIFTI') Files
Functions for the input/output and visualization of medical imaging data in the form of 'CIFTI' files <https://www.nitrc.org/projects/cifti/>.
Maintained by John Muschelli. Last updated 5 years ago.
2.9 match 3 stars 5.76 score 96 scriptsohdsi
FeatureExtraction:Generating Features for a Cohort
An R interface for generating features for a cohort using data in the Common Data Model. Features can be constructed using default or custom made feature definitions. Furthermore it's possible to aggregate features and get the summary statistics.
Maintained by Ger Inberg. Last updated 5 months ago.
1.6 match 62 stars 10.30 score 209 scripts 1 dependentsbioc
cfTools:Informatics Tools for Cell-Free DNA Study
The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.
Maintained by Ran Hu. Last updated 5 months ago.
softwarebiomedicalinformaticsepigeneticssequencingmethylseqdnamethylationdifferentialmethylationcpp
2.9 match 7 stars 5.32 score 2 scriptsohdsi
ParallelLogger:Support for Parallel Computation, Logging, and Function Automation
Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk, and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in parallel).
Maintained by Martijn Schuemie. Last updated 6 months ago.
1.6 match 12 stars 9.18 score 87 scripts 11 dependentsohdsi
Andromeda:Asynchronous Disk-Based Representation of Massive Data
Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Maintained by Martijn Schuemie. Last updated 7 months ago.
1.6 match 11 stars 9.18 score 57 scripts 7 dependentsohdsi
Cyclops:Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis
This model fitting tool incorporates cyclic coordinate descent and majorization-minimization approaches to fit a variety of regression models found in large-scale observational healthcare data. Implementations focus on computational optimization and fine-scale parallelization to yield efficient inference in massive datasets. Please see: Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.
Maintained by Marc A. Suchard. Last updated 4 months ago.
1.5 match 39 stars 9.05 score 73 scripts 4 dependents
kwstat
agridat:Agricultural Datasets
Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.
Maintained by Kevin Wright. Last updated 28 days ago.
1.3 match 125 stars 11.02 score 1.7k scripts 2 dependents
laperez
Clustering:Techniques for Evaluating Clustering
The design of this package allows us to run different clustering packages and compare the results between them, to determine which algorithm behaves best from the data provided. See Martos, L.A.P., García-Vico, Á.M., González, P. et al.(2023) <doi:10.1007/s13748-022-00294-2> "Clustering: an R library to facilitate the analysis and comparison of cluster algorithms.", Martos, L.A.P., García-Vico, Á.M., González, P. et al. "A Multiclustering Evolutionary Hyperrectangle-Based Algorithm" <doi:10.1007/s44196-023-00341-3> and L.A.P., García-Vico, Á.M., González, P. et al. "An Evolutionary Fuzzy System for Multiclustering in Data Streaming" <doi:10.1016/j.procs.2023.12.058>.
Maintained by Luis Alfonso Perez Martos. Last updated 11 months ago.
3.1 match 5 stars 4.04 score 7 scriptsohdsi
CohortGenerator:Cohort Generation for the OMOP Common Data Model
Generate cohorts and subsets using an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database. Cohorts are defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).
Maintained by Anthony Sena. Last updated 6 months ago.
1.6 match 13 stars 7.91 score 165 scriptsbioc
CINdex:Chromosome Instability Index
The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.
Maintained by Yuriy Gusev. Last updated 5 months ago.
softwarecopynumbervariationgenomicvariationacghmicroarraygeneticssequencing
3.0 match 4.08 score 2 scripts
mqnjqrid
drpop:Efficient and Doubly Robust Population Size Estimation
Estimation of the total population size from capture-recapture data efficiently and with low bias implementing the methods from Das M, Kennedy EH, and Jewell NP (2021) <arXiv:2104.14091>. The estimator is doubly robust against errors in the estimation of the intermediate nuisance parameters. Users can choose from the flexible estimation models provided in the package, or use any other preferred model.
Maintained by Manjari Das. Last updated 3 years ago.
3.3 match 5 stars 3.40 score 2 scripts
nowosad
sabre:Spatial Association Between Regionalizations
Calculates a degree of spatial association between regionalizations or categorical maps using the information-theoretical V-measure (Nowosad and Stepinski (2018) <doi:10.1080/13658816.2018.1511794>). It also offers an R implementation of the MapCurve method (Hargrove et al. (2006) <doi:10.1007/s10109-006-0025-x>).
Maintained by Jakub Nowosad. Last updated 3 months ago.
entropypolygonsregionalizationsspatialspatial-analysis
1.6 match 36 stars 6.95 score 25 scriptsohdsi
Eunomia:Standard Dataset Manager for Observational Medical Outcomes Partnership Common Data Model Sample Datasets
Facilitates access to sample datasets from the 'EunomiaDatasets' repository (<https://github.com/ohdsi/EunomiaDatasets>).
Maintained by Frank DeFalco. Last updated 11 months ago.
1.6 match 43 stars 6.73 score 139 scripts
egenn
rtemisbio:rtemis Bio-informatics
Bio-informatics utilities
Maintained by E.D. Gennatas. Last updated 5 months ago.
4.0 match 1 stars 2.60 score 1 scriptsbioc
sparrow:Take command of set enrichment analyses through a unified interface
Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.
Maintained by Steve Lianoglou. Last updated 3 months ago.
genesetenrichmentpathwaysbioinformaticsgsea
1.6 match 21 stars 6.58 score 13 scripts
miracum
DQAstats:Core Functions for Data Quality Assessment
Perform data quality assessment ('DQA') of electronic health records ('EHR'). Publication: Kapsner et al. (2021) <doi:10.1055/s-0041-1733847>.
Maintained by Lorenz A. Kapsner. Last updated 14 days ago.
1.5 match 9 stars 6.55 score 4 scripts 1 dependents
cran
blockmodeling:Generalized and Classical Blockmodeling of Valued Networks
This is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted: Žiberna (2007)<doi:10.1016/j.socnet.2006.04.002>, Žiberna (2008)<doi:10.1080/00222500701790207>, Žiberna (2014)<doi:10.1016/j.socnet.2014.04.002>.
Maintained by Aleš Žiberna. Last updated 2 years ago.
3.5 match 2.78 score 12 dependentsohdsi
EvidenceSynthesis:Synthesizing Causal Evidence in a Distributed Research Network
Routines for combining causal effect estimates and study diagnostics across multiple data sites in a distributed study, without sharing patient-level data. Allows for normal and non-normal approximations of the data-site likelihood of the effect parameter.
Maintained by Martijn Schuemie. Last updated 6 months ago.
1.6 match 8 stars 5.87 score 31 scripts
r-spatialecology
belg:Boltzmann Entropy of a Landscape Gradient
Calculates the Boltzmann entropy of a landscape gradient. This package uses the analytical method created by Gao, P., Zhang, H. and Li, Z., 2018 (<doi:10.1111/tgis.12315>) and by Gao, P. and Li, Z., 2019 (<doi:10.1007/s10980-019-00854-3>). It also extend the original ideas by allowing calculations on data with missing values.
Maintained by Jakub Nowosad. Last updated 2 years ago.
entropylandscaperasterspatialcpp
1.6 match 19 stars 5.80 score 11 scripts 1 dependents
mamut86
diffusion:Forecast the Diffusion of New Products
Various diffusion models to forecast new product growth. Currently the package contains Bass, Gompertz, Gamma/Shifted Gompertz and Weibull curves. See Meade and Islam (2006) <doi:10.1016/j.ijforecast.2006.01.005>.
Maintained by Oliver Schaer. Last updated 11 months ago.
diffusiondiffusion-modelsforecastinggrowth-curve-modelslifecyclenew-product
1.5 match 8 stars 5.54 score 29 scripts
fdefalco
Achilles:Achilles Data Source Characterization
Automated Characterization of Health Information at Large-Scale Longitudinal Evidence Systems. Creates a descriptive statistics summary for an Observational Medical Outcomes Partnership Common Data Model standardized data source. This package includes functions for executing summary queries on the specified data source and exporting reporting content for use across a variety of Observational Health Data Sciences and Informatics community applications.
Maintained by Frank DeFalco. Last updated 2 years ago.
2.1 match 4.06 score 115 scriptsmiracum
DIZutils:Utilities for 'DIZ' R Package Development
Utility functions used for the R package development infrastructure inside the data integration centers ('DIZ') to standardize and facilitate repetitive tasks such as setting up a database connection or issuing notification messages and to avoid redundancy.
Maintained by Jonathan M. Mang. Last updated 4 months ago.
1.5 match 3 stars 5.03 score 5 scripts 2 dependentsohdsi
CohortExplorer:Explorer of Profiles of Patients in a Cohort
This software tool is designed to extract data from a randomized subset of individuals within a cohort and make it available for exploration in a shiny application environment. It retrieves date-stamped, event-level records from one or more data sources that represent patient data in the Observational Medical Outcomes Partnership (OMOP) data model format. This tool features a user-friendly interface that enables users to efficiently explore the extracted profiles, thereby facilitating applications, such as reviewing structured profiles.
Maintained by Gowtham Rao. Last updated 1 years ago.
1.7 match 3 stars 4.18 score 3 scriptsohdsi
CohortAlgebra:Use of Interval Algebra to Create New Cohort(s) from Existing Cohorts
This software tool is designed to generate new cohorts utilizing data from previously instantiated cohorts. It employs interval algebra operators such as UNION, INTERSECT, and MINUS to manipulate the data within the instantiated cohorts and create new cohorts.
Maintained by Gowtham Rao. Last updated 21 days ago.
1.7 match 1 stars 4.00 scoremiracum
DQAgui:Graphical User Interface for Data Quality Assessment
A graphical user interface (GUI) to the functions implemented in the R package 'DQAstats'. Publication: Mang et al. (2021) <doi:10.1186/s12911-022-01961-z>.
Maintained by Lorenz A. Kapsner. Last updated 1 months ago.
1.5 match 2 stars 4.15 score 10 scriptsmiracum
DIZtools:Lightweight Utilities for 'DIZ' R Package Development
Lightweight utility functions used for the R package development infrastructure inside the data integration centers ('DIZ') to standardize and facilitate repetitive tasks such as setting up a database connection or issuing notification messages and to avoid redundancy.
Maintained by Jonathan M. Mang. Last updated 1 years ago.
1.5 match 3 stars 4.13 score 2 scripts 3 dependentsnowosad
rgeopat2:Additional Functions for 'GeoPAT' 2
Supports analysis of spatial data processed with the 'GeoPAT' 2 software <https://github.com/Nowosad/geopat2>. Available features include creation of a grid based on the 'GeoPAT' 2 grid header file and reading a 'GeoPAT' 2 text outputs.
Maintained by Jakub Nowosad. Last updated 1 years ago.
1.6 match 10 stars 3.81 score 13 scripts
joundso
cleaR:Clean the R Console and Environment
Small package to clean the R console and the R environment with the call of just one function.
Maintained by Jonathan M. Mang. Last updated 1 years ago.
1.6 match 3.78 score 3 scripts 4 dependents
stla
cascadeSelect:A Cascade Select Input for 'Shiny'
Provides a cascade select widget for usage in 'Shiny' applications. This is useful for selection of hierarchical choices (e.g. continent, country, city). It is taken from the 'JavaScript' library 'PrimeReact'.
Maintained by Stéphane Laurent. Last updated 2 years ago.
1.7 match 6 stars 3.48 score 8 scriptsjoundso
requiRements:Helper Package to Install Packages for R
Helper function to install packages for R using an external 'requirements.txt' or a string containing diverse packages from several resources like Github or CRAN.
Maintained by Jonathan M. Mang. Last updated 2 years ago.
1.6 match 9 stars 3.65 score 7 scripts
jreps
OhdsiShinyAppBuilder:Viewing Observational Health Data Sciences and Informatics Results via 'shiny' Modules
Users can build a single 'shiny' app for exploring population characterization, population-level causal effect estimation, and patient-level prediction results generated via the R analyses packages in 'HADES' (see <https://ohdsi.github.io/Hades/>). Learn more about 'OhdsiShinyAppBuilder' at <https://ohdsi.github.io/OhdsiShinyAppBuilder/>.
Maintained by Jenna Reps. Last updated 3 months ago.
2.8 match 2.00 score 1 scriptsohdsi
DatabaseConnectorJars:JAR Dependencies for the 'DatabaseConnector' Package
Provides external JAR dependencies for the 'DatabaseConnector' package.
Maintained by Martijn Schuemie. Last updated 2 years ago.
1.5 match 1 stars 3.00 score
aprilnguyen1
icdcomorbid:Mapping ICD Codes to Comorbidity
Provides tools for mapping International Classification of Diseases codes to comorbidity, enabling the identification and analysis of various medical conditions within healthcare data.
Maintained by April Nguyen. Last updated 7 months ago.
1.6 match 2.70 scoreropensci
emld:Ecological Metadata as Linked Data
This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.
Maintained by Carl Boettiger. Last updated 4 years ago.
0.5 match 13 stars 7.63 score 69 scripts 8 dependentsohdsi
ResultModelManager:Result Model Manager
Database data model management utilities for R packages in the Observational Health Data Sciences and Informatics program <https://ohdsi.org>. 'ResultModelManager' provides utility functions to allow package maintainers to migrate existing SQL database models, export and import results in consistent patterns.
Maintained by Jamie Gilbert. Last updated 6 months ago.
0.5 match 4 stars 7.38 score 9 scripts 3 dependents
roux-ohdsi
allofus:Interface for 'All of Us' Researcher Workbench
Streamline use of the 'All of Us' Researcher Workbench (<https://www.researchallofus.org/data-tools/workbench/>)with tools to extract and manipulate data from the 'All of Us' database. Increase interoperability with the Observational Health Data Science and Informatics ('OHDSI') tool stack by decreasing reliance of 'All of Us' tools and allowing for cohort creation via 'Atlas'. Improve reproducible and transparent research using 'All of Us'.
Maintained by Rob Cavanaugh. Last updated 4 months ago.
0.5 match 16 stars 7.19 score 30 scriptsmuschellij2
gifti:Reads in 'Neuroimaging' 'GIFTI' Files with Geometry Information
Functions to read in the geometry format under the 'Neuroimaging' 'Informatics' Technology Initiative ('NIfTI'), called 'GIFTI' <https://www.nitrc.org/projects/gifti/>. These files contain surfaces of brain imaging data.
Maintained by John Muschelli. Last updated 3 years ago.
0.5 match 4 stars 6.99 score 82 scripts 10 dependents
aleszib
dBlockmodeling:Deterministic Blockmodeling of Signed, One-Mode and Two-Mode Networks
It contains functions to apply blockmodeling of signed (positive and negative weights are assigned to the links), one-mode and valued one-mode and two-mode (two sets of nodes are considered, e.g. employees and organizations) networks (Brusco et al. (2019) <doi:10.1111/bmsp.12192>).
Maintained by Aleš Žiberna. Last updated 2 years ago.
3.5 match 1 stars 1.00 score 1 scripts
sjmack
HLAtools:Toolkit for HLA Immunogenomics
A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.
Maintained by Steven Mack. Last updated 13 days ago.
0.5 match 4 stars 6.21 score 7 scripts 1 dependents
msuchard
IterativeHardThresholding:Iterative Hard Thresholding Extensions to Cyclops
Fits large-scale regression models with a penalty that restricts the maximum number of non-zero regression coefficients to a prespecified value. While Chu et al (2020) <doi:10.1093/gigascience/giaa044> describe the basic algorithm, this package uses Cyclops for an efficient implementation.
Maintained by Marc A. Suchard. Last updated 3 years ago.
1.6 match 1.70 score 3 scriptsmsuchard
BrokenAdaptiveRidge:Broken Adaptive Ridge Regression with Cyclops
Approximates best-subset selection (L0) regression with an iteratively adaptive Ridge (L2) penalty for large-scale models. This package uses Cyclops for an efficient implementation and the iterative method is described in Kawaguchi et al (2020) <doi:10.1002/sim.8438> and Li et al (2021) <doi:10.1016/j.jspi.2020.12.001>.
Maintained by Marc A. Suchard. Last updated 2 years ago.
1.6 match 1.70 score 5 scriptsmsuchard
RcppXsimd:Xsimd C++ Header-Only Library Files
This header-only library provides modern, portable C++ wrappers for SIMD intrinsics and parallelized, optimized math implementations (SSE, AVX, NEON, AVX512). By placing this library in this package, we offer an efficient distribution system for Xsimd <https://github.com/xtensor-stack/xsimd> for R packages using CRAN.
Maintained by Marc A. Suchard. Last updated 4 years ago.
1.5 match 1.70 score 6 scripts
hannahlowens
climateStability:Estimating Climate Stability from Climate Model Data
Climate stability measures are not formalized in the literature and tools for generating stability metrics from existing data are nascent. This package provides tools for calculating climate stability from raster data encapsulating climate change as a series of time slices. The methods follow Owens and Guralnick <doi:10.17161/bi.v14i0.9786> Biodiversity Informatics.
Maintained by Hannah Owens. Last updated 2 years ago.
0.5 match 7 stars 5.01 score 29 scripts
huangzhii
lmQCM:An Algorithm for Gene Co-Expression Analysis
Implementation based on Zhang, Jie & Huang, Kun (2014) <doi:10.4137/CIN.S14021> Normalized ImQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers. Cancer informatics, 13, CIN-S14021.
Maintained by Zhi Huang. Last updated 2 years ago.
0.5 match 5 stars 4.48 score 12 scripts
bupaverse
bupaverse:Easily Install and Load the 'bupaverse'
The 'bupaverse' is an open-source, integrated suite of R-packages for handling and analysing business process data, developed by the Business Informatics research group at Hasselt University, Belgium. Profoundly inspired by the 'tidyverse' package, the 'bupaverse' package is designed to facilitate the installation and loading of multiple 'bupaverse' packages in a single step. Learn more about 'bupaverse' at the <https://bupar.net> homepage.
Maintained by Gert Janssenswillen. Last updated 2 years ago.
0.5 match 2 stars 4.32 score 21 scripts
end-to-end-provenance
provSummarizeR:Summarizes Provenance Related to Inputs and Outputs of a Script or Console Commands
Reads the provenance collected by the 'rdtLite' or 'rdt' packages, or other tools providing compatible PROV JSON output, created by the execution of a script or a console session, and provides a human-readable summary identifying the input and output files, the scripts used (if any), errors and warnings produced, and the environment in which it was executed. It can also optionally package all the files into a zip file. The exact format of the PROV JSON file created by 'rdtLite' and 'rdt' is described in <https://github.com/End-to-end-provenance/ExtendedProvJson>. More information about 'rdtLite' and associated tools is available at <https://github.com/End-to-end-provenance/> and Lerner, Boose, and Perez (2018), Using Introspection to Collect Provenance in R, Informatics, <doi: 10.3390/informatics5010012>.
Maintained by Emery Boose. Last updated 3 years ago.
0.5 match 4.18 score 7 scriptsend-to-end-provenance
provViz:Provenance Visualizer
Displays provenance graphically for provenance collected by the 'rdt' or 'rdtLite' packages, or other tools providing compatible PROV JSON output. The exact format of the JSON created by 'rdt' and 'rdtLite' is described in <https://github.com/End-to-end-provenance/ExtendedProvJson>. More information about rdtLite and associated tools is available at <https://github.com/End-to-end-provenance/> and Barbara Lerner, Emery Boose, and Luis Perez (2018), Using Introspection to Collect Provenance in R, Informatics, <doi: 10.3390/informatics5010012>.
Maintained by Barbara Lerner. Last updated 3 years ago.
0.5 match 3.48 score 2 scripts 1 dependents
jfwambaugh
invivoPKfit:Fits Toxicokinetic Models to In Vivo PK Data Sets
Takes in vivo toxicokinetic concentration-time data and fits parameters of 1-compartment and 2-compartment models for each chemical. These methods are described in detail in "Informatics for Toxicokinetics" (submitted).
Maintained by John Wambaugh. Last updated 2 months ago.
0.5 match 2.60 score 4 scriptscran
smoothy:Automatic Estimation of the Most Likely Drug Combination using Smooth Algorithm
A flexible moving average algorithm for modeling drug exposure in pharmacoepidemiology studies as presented in the article: Ouchi, D., Giner-Soriano, M., Gómez-Lumbreras, A., Vedia Urgell, C.,Torres, F., & Morros, R. (2022). "Automatic Estimation of the Most Likely Drug Combination in Electronic Health Records Using the Smooth Algorithm : Development and Validation Study." JMIR medical informatics, 10(11), e37976. <doi:10.2196/37976>.
Maintained by Dan Ouchi. Last updated 2 years ago.
0.5 match 2.04 score 11 scriptscran
RESTK:An Implementation of the RESTK Algorithm
Implementation of the RESTK algorithm based on Markov's Inequality from Vilardell, Sergi, Serra, Isabel, Mezzetti, Enrico, Abella, Jaume, Cazorla, Francisco J. and Del Castillo, J. (2022). "Using Markov's Inequality with Power-Of-k Function for Probabilistic WCET Estimation". In 34th Euromicro Conference on Real-Time Systems (ECRTS 2022). Leibniz International Proceedings in Informatics (LIPIcs) 231 20:1-20:24. <doi:10.4230/LIPIcs.ECRTS.2022.20>. This work has been supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 772773).
Maintained by Sergi Vilardell. Last updated 4 days ago.
0.5 match 1.00 score