Showing 200 of total 211 results (show query)
rinterface
shinydashboardPlus:Add More 'AdminLTE2' Components to 'shinydashboard'
Extend 'shinydashboard' with 'AdminLTE2' components. 'AdminLTE2' is a free 'Bootstrap 3' dashboard template available at <https://adminlte.io>. Customize boxes, add timelines and a lot more.
Maintained by David Granjon. Last updated 8 months ago.
dashboardhacktoberfest2022shinyshiny-appsshinydashboard
461 stars 13.82 score 1.1k scripts 28 dependents
bioc
iSEE:Interactive SummarizedExperiment Explorer
Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.
Maintained by Kevin Rue-Albrecht. Last updated 27 days ago.
cellbasedassaysclusteringdimensionreductionfeatureextractiongeneexpressionguiimmunooncologyshinyappssinglecelltranscriptiontranscriptomicsvisualizationdimension-reductionfeature-extractiongene-expressionhacktoberfesthuman-cell-atlasshinysingle-cell
225 stars 12.86 score 380 scripts 9 dependentsbioc
PharmacoGx:Analysis of Large-Scale Pharmacogenomic Data
Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.
Maintained by Benjamin Haibe-Kains. Last updated 3 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationdatasetspharmacogenomicpharmacogxcpp
68 stars 11.39 score 442 scripts 3 dependentsbioc
pcaExplorer:Interactive Visualization of RNA-seq Data Using a Principal Components Approach
This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.
Maintained by Federico Marini. Last updated 3 months ago.
immunooncologyvisualizationrnaseqdimensionreductionprincipalcomponentqualitycontrolguireportwritingshinyappsbioconductorprincipal-componentsreproducible-researchrna-seq-analysisrna-seq-datashinytranscriptomeuser-friendly
56 stars 9.63 score 180 scriptsbioc
cytomapper:Visualization of highly multiplexed imaging data in R
Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.
Maintained by Lasse Meyer. Last updated 5 months ago.
immunooncologysoftwaresinglecellonechanneltwochannelmultiplecomparisonnormalizationdataimportbioimagingimaging-mass-cytometrysingle-cellspatial-analysis
32 stars 9.61 score 354 scripts 5 dependents
wenchao-ma
GDINA:The Generalized DINA Model Framework
A set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070> for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre <DOI:10.1177/0146621613479818> for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided. For tutorials, please check Ma and de la Torre (2020) <DOI:10.18637/jss.v093.i14>, Ma and de la Torre (2019) <DOI:10.1111/emip.12262>, Ma (2019) <DOI:10.1007/978-3-030-05584-4_29> and de la Torre and Akbay (2019).
Maintained by Wenchao Ma. Last updated 2 months ago.
cdmcognitive-diagnosisdcmdina-modeldinoestimation-modelsgdinaitem-response-theorypsychometricsopenblascpp
30 stars 8.92 score 94 scripts 6 dependentsbioc
iCOBRA:Comparison and Visualization of Ranking and Assignment Methods
This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. Various types of performance plots can be generated programmatically. The package also contains a shiny application for interactive exploration of results.
Maintained by Charlotte Soneson. Last updated 3 months ago.
14 stars 8.86 score 192 scripts 1 dependentsbioc
piano:Platform for integrative analysis of omics data
Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.
Maintained by Leif Varemo Wigge. Last updated 5 months ago.
microarraypreprocessingqualitycontroldifferentialexpressionvisualizationgeneexpressiongenesetenrichmentpathwaysbioconductorbioconductor-packagebioinformaticsgene-set-enrichmenttranscriptomics
13 stars 8.30 score 183 scripts 7 dependentsbioc
ExploreModelMatrix:Graphical Exploration of Design Matrices
Given a sample data table and a design formula, ExploreModelMatrix generates an interactive application for exploration of the resulting design matrix. This can be helpful for interpreting model coefficients and constructing appropriate contrasts in (generalized) linear models. Static visualizations can also be generated.
Maintained by Charlotte Soneson. Last updated 3 months ago.
experimentaldesignregressiondifferentialexpressionshinyapps
37 stars 8.16 score 81 scriptsbioc
compcodeR:RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.
Maintained by Charlotte Soneson. Last updated 3 months ago.
immunooncologyrnaseqdifferentialexpression
12 stars 8.10 score 26 scripts
tychobra
polished:Authentication and Hosting for 'shiny' Apps
Authentication, user administration, hosting, and additional infrastructure for 'shiny' apps. See <https://polished.tech> for additional documentation and examples.
Maintained by Andy Merlino. Last updated 12 days ago.
233 stars 8.09 score 75 scriptsbioc
spicyR:Spatial analysis of in situ cytometry data
The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.
Maintained by Ellis Patrick. Last updated 28 days ago.
singlecellcellbasedassaysspatial
9 stars 8.02 score 57 scripts 1 dependents
thibautjombart
treespace:Statistical Exploration of Landscapes of Phylogenetic Trees
Tools for the exploration of distributions of phylogenetic trees. This package includes a 'shiny' interface which can be started from R using treespaceServer(). For further details see Jombart et al. (2017) <DOI:10.1111/1755-0998.12676>.
Maintained by Michelle Kendall. Last updated 2 years ago.
29 stars 7.88 score 63 scripts 1 dependentsbioc
debrowser:Interactive Differential Expresion Analysis Browser
Bioinformatics platform containing interactive plots and tables for differential gene and region expression studies. Allows visualizing expression data much more deeply in an interactive and faster way. By changing the parameters, users can easily discover different parts of the data that like never have been done before. Manually creating and looking these plots takes time. With DEBrowser users can prepare plots without writing any code. Differential expression, PCA and clustering analysis are made on site and the results are shown in various plots such as scatter, bar, box, volcano, ma plots and Heatmaps.
Maintained by Alper Kucukural. Last updated 5 months ago.
sequencingchipseqrnaseqdifferentialexpressiongeneexpressionclusteringimmunooncology
61 stars 7.80 score 65 scriptsbioc
LACE:Longitudinal Analysis of Cancer Evolution (LACE)
LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points.
Maintained by Davide Maspero. Last updated 17 days ago.
biomedicalinformaticssinglecellsomaticmutation
15 stars 7.75 score 3 scriptsbioc
signeR:Empirical Bayesian approach to mutational signature discovery
The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variation (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.
Maintained by Renan Valieris. Last updated 5 months ago.
genomicvariationsomaticmutationstatisticalmethodvisualizationbioconductorbioinformaticsopenblascpp
13 stars 7.67 score 22 scriptsbioc
imcRtools:Methods for imaging mass cytometry data analysis
This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.
Maintained by Daniel Schulz. Last updated 5 months ago.
immunooncologysinglecellspatialdataimportclusteringimcsingle-cell
24 stars 7.58 score 126 scripts
bioc
gDRimport:Package for handling the import of dose-response data
The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats.
Maintained by Arkadiusz Gladki. Last updated 6 days ago.
softwareinfrastructuredataimport
3 stars 7.32 score 5 scripts 1 dependentsbioc
iSEEu:iSEE Universe
iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications.
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
immunooncologyvisualizationguidimensionreductionfeatureextractionclusteringtranscriptiongeneexpressiontranscriptomicssinglecellcellbasedassayshacktoberfest
9 stars 7.15 score 35 scripts 1 dependentsbioc
DEP:Differential Enrichment analysis of Proteomics data
This package provides an integrated analysis workflow for robust and reproducible analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment. It requires tabular input (e.g. txt files) as generated by quantitative analysis softwares of raw mass spectrometry data, such as MaxQuant or IsobarQuant. Functions are provided for data preparation, filtering, variance normalization and imputation of missing values, as well as statistical testing of differentially enriched / expressed proteins. It also includes tools to check intermediate steps in the workflow, such as normalization and missing values imputation. Finally, visualization tools are provided to explore the results, including heatmap, volcano plot and barplot representations. For scientists with limited experience in R, the package also contains wrapper functions that entail the complete analysis workflow and generate a report. Even easier to use are the interactive Shiny apps that are provided by the package.
Maintained by Arne Smits. Last updated 5 months ago.
immunooncologyproteomicsmassspectrometrydifferentialexpressiondatarepresentation
7.10 score 628 scriptsbioc
systemPipeShiny:systemPipeShiny: An Interactive Framework for Workflow Management and Visualization
systemPipeShiny (SPS) extends the widely used systemPipeR (SPR) workflow environment with a versatile graphical user interface provided by a Shiny App. This allows non-R users, such as experimentalists, to run many systemPipeR’s workflow designs, control, and visualization functionalities interactively without requiring knowledge of R. Most importantly, SPS has been designed as a general purpose framework for interacting with other R packages in an intuitive manner. Like most Shiny Apps, SPS can be used on both local computers as well as centralized server-based deployments that can be accessed remotely as a public web service for using SPR’s functionalities with community and/or private data. The framework can integrate many core packages from the R/Bioconductor ecosystem. Examples of SPS’ current functionalities include: (a) interactive creation of experimental designs and metadata using an easy to use tabular editor or file uploader; (b) visualization of workflow topologies combined with auto-generation of R Markdown preview for interactively designed workflows; (d) access to a wide range of data processing routines; (e) and an extendable set of visualization functionalities. Complex visual results can be managed on a 'Canvas Workbench’ allowing users to organize and to compare plots in an efficient manner combined with a session snapshot feature to continue work at a later time. The present suite of pre-configured visualization examples. The modular design of SPR makes it easy to design custom functions without any knowledge of Shiny, as well as extending the environment in the future with contributions from the community.
Maintained by Le Zhang. Last updated 5 months ago.
shinyappsinfrastructuredataimportsequencingqualitycontrolreportwritingexperimentaldesignclusteringbioconductorbioconductor-packagedata-visualizationshinysystempiper
34 stars 7.04 score 36 scripts
cb4ds
periscope:Enterprise Streamlined 'Shiny' Application Framework
An enterprise-targeted scalable and UI-standardized 'shiny' framework including a variety of developer convenience functions with the goal of both streamlining robust application development while assisting with creating a consistent user experience regardless of application or developer.
Maintained by Constance Brett. Last updated 2 months ago.
18 stars 7.02 score 73 scripts
sylvainschmitt
SSDM:Stacked Species Distribution Modelling
Allows to map species richness and endemism based on stacked species distribution models (SSDM). Individuals SDMs can be created using a single or multiple algorithms (ensemble SDMs). For each species, an SDM can yield a habitat suitability map, a binary map, a between-algorithm variance map, and can assess variable importance, algorithm accuracy, and between- algorithm correlation. Methods to stack individual SDMs include summing individual probabilities and thresholding then summing. Thresholding can be based on a specific evaluation metric or by drawing repeatedly from a Bernoulli distribution. The SSDM package also provides a user-friendly interface.
Maintained by Sylvain Schmitt. Last updated 11 months ago.
44 stars 6.99 score 44 scriptsbioc
alevinQC:Generate QC Reports For Alevin Output
Generate QC reports summarizing the output from an alevin, alevin-fry, or simpleaf run. Reports can be generated as html or pdf files, or as shiny applications.
Maintained by Charlotte Soneson. Last updated 3 months ago.
32 stars 6.91 score 21 scriptsbioc
pRolocGUI:Interactive visualisation of spatial proteomics data
The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.
Maintained by Lisa Breckels. Last updated 5 months ago.
8 stars 6.90 score 3 scriptsbioc
ideal:Interactive Differential Expression AnaLysis
This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.
Maintained by Federico Marini. Last updated 3 months ago.
immunooncologygeneexpressiondifferentialexpressionrnaseqsequencingvisualizationqualitycontrolguigenesetenrichmentreportwritingshinyappsbioconductordifferential-expressionreproducible-researchrna-seqrna-seq-analysisshinyuser-friendly
29 stars 6.78 score 5 scripts
cschwem2er
stminsights:A 'Shiny' Application for Inspecting Structural Topic Models
This app enables interactive validation, interpretation and visualization of structural topic models from the 'stm' package by Roberts and others (2014) <doi:10.1111/ajps.12103>. It also includes helper functions for model diagnostics and extracting data from effect estimates.
Maintained by Carsten Schwemmer. Last updated 9 months ago.
natural-language-processingshinytopic-modeling
117 stars 6.69 score 84 scriptsbioc
lisaClust:lisaClust: Clustering of Local Indicators of Spatial Association
lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.
Maintained by Ellis Patrick. Last updated 4 months ago.
singlecellcellbasedassaysspatial
3 stars 6.64 score 48 scriptsbioc
Xeva:Analysis of patient-derived xenograft (PDX) data
The Xeva package provides efficient and powerful functions for patient-drived xenograft (PDX) based pharmacogenomic data analysis. This package contains a set of functions to perform analysis of patient-derived xenograft data. This package was developed by the BHKLab, for further information please see our documentation.
Maintained by Benjamin Haibe-Kains. Last updated 12 days ago.
geneexpressionpharmacogeneticspharmacogenomicssoftwareclassification
11 stars 6.48 score 17 scripts
husson
Factoshiny:Perform Factorial Analysis from 'FactoMineR' with a Shiny Application
Perform factorial analysis with a menu and draw graphs interactively thanks to 'FactoMineR' and a Shiny application.
Maintained by Francois Husson. Last updated 3 months ago.
9 stars 6.46 score 152 scriptsbioc
SpliceWiz:interactive analysis and visualization of alternative splicing in R
The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.
Maintained by Alex Chit Hei Wong. Last updated 20 days ago.
softwaretranscriptomicsrnaseqalternativesplicingcoveragedifferentialsplicingdifferentialexpressionguisequencingcppopenmp
16 stars 6.41 score 8 scriptsbioc
CoreGx:Classes and Functions to Serve as the Basis for Other 'Gx' Packages
A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmacoSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
softwarepharmacogenomicsclassificationsurvival
6.36 score 63 scripts 6 dependents
thewileylab
ReviewR:A Light-Weight, Portable Tool for Reviewing Individual Patient Records
A portable Shiny tool to explore patient-level electronic health record data and perform chart review in a single integrated framework. This tool supports browsing clinical data in many different formats including multiple versions of the 'OMOP' common data model as well as the 'MIMIC-III' data model. In addition, chart review information is captured and stored securely via the Shiny interface in a 'REDCap' (Research Electronic Data Capture) project using the 'REDCap' API. See the 'ReviewR' website for additional information, documentation, and examples.
Maintained by David Mayer. Last updated 2 years ago.
24 stars 6.33 score 6 scripts
phuse-org
sendigR:Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets
A system enables cross study Analysis by extracting and filtering study data for control animals from 'CDISC' 'SEND' Study Repository. These data types are supported: Body Weights, Laboratory test results and Microscopic findings. These database types are supported: 'SQLite' and 'Oracle'.
Maintained by Wenxian Wang. Last updated 26 days ago.
12 stars 6.28 score 6 scriptsbioc
iSEEtree:Interactive visualisation for microbiome data
iSEEtree is an extension of iSEE for the TreeSummarizedExperiment data container. It provides interactive panel designs to explore hierarchical datasets, such as the microbiome and cell lines.
Maintained by Giulio Benedetti. Last updated 13 days ago.
softwarevisualizationmicrobiomeguishinyappsdataimportshiny-appsvisualisation
3 stars 6.28 score 5 scriptsbioc
spatialHeatmap:spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data. A description of the project is available here: https://spatialheatmap.org.
Maintained by Jianhai Zhang. Last updated 4 months ago.
spatialvisualizationmicroarraysequencinggeneexpressiondatarepresentationnetworkclusteringgraphandnetworkcellbasedassaysatacseqdnaseqtissuemicroarraysinglecellcellbiologygenetarget
5 stars 6.26 score 12 scripts
tzerk
RLumShiny:'Shiny' Applications for the R Package 'Luminescence'
A collection of 'shiny' applications for the R package 'Luminescence'. These mainly, but not exclusively, include applications for plotting chronometric data from e.g. luminescence or radiocarbon dating. It further provides access to bootstraps tooltip and popover functionality and contains the 'jscolor.js' library with a custom 'shiny' output binding.
Maintained by Christoph Burow. Last updated 7 days ago.
bootstrapjscolorluminescenceluminescence-datingshinyshiny-applicationstooltip
7 stars 6.23 score 67 scripts 2 dependents
tidymodels
shinymodels:Interactive Assessments of Models
Launch a 'shiny' application for 'tidymodels' results. For classification or regression models, the app can be used to determine if there is lack of fit or poorly predicted points.
Maintained by Simon Couch. Last updated 5 months ago.
48 stars 6.21 score 48 scripts
patzaw
TKCat:Tailored Knowledge Catalog
Facilitate the management of data from knowledge resources that are frequently used alone or together in research environments. In 'TKCat', knowledge resources are manipulated as modeled database (MDB) objects. These objects provide access to the data tables along with a general description of the resource and a detail data model documenting the tables, their fields and their relationships. These MDBs are then gathered in catalogs that can be easily explored an shared. Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and create new catalogs suited for specific needs.
Maintained by Patrice Godard. Last updated 6 days ago.
5 stars 6.13 score 27 scriptsbioc
simpleSeg:A package to perform simple cell segmentation
Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images.
Maintained by Ellis Patrick. Last updated 5 months ago.
classificationsurvivalsinglecellnormalizationspatialspatial-statistics
6.06 score 19 scripts 2 dependents
zhenkewu
baker:"Nested Partially Latent Class Models"
Provides functions to specify, fit and visualize nested partially-latent class models ( Wu, Deloria-Knoll, Hammitt, and Zeger (2016) <doi:10.1111/rssc.12101>; Wu, Deloria-Knoll, and Zeger (2017) <doi:10.1093/biostatistics/kxw037>; Wu and Chen (2021) <doi:10.1002/sim.8804>) for inference of population disease etiology and individual diagnosis. In the motivating Pneumonia Etiology Research for Child Health (PERCH) study, because both quantities of interest sum to one hundred percent, the PERCH scientists frequently refer to them as population etiology pie and individual etiology pie, hence the name of the package.
Maintained by Zhenke Wu. Last updated 11 months ago.
bayesiancase-controllatent-class-analysisjagscpp
8 stars 6.00 score 21 scriptsbioc
DiscoRhythm:Interactive Workflow for Discovering Rhythmicity in Biological Data
Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. Supporting functions are available for quality control, dimensionality reduction, spectral analysis, and analysis of experimental replicates. Contains a R Shiny web interface to execute all workflow steps.
Maintained by Matthew Carlucci. Last updated 5 months ago.
softwaretimecoursequalitycontrolvisualizationguiprincipalcomponentbioconductordata-visualizationoscillationsrhythm-detectionwebapp
13 stars 5.89 score 9 scriptsbioc
ChromSCape:Analysis of single-cell epigenomics datasets with a Shiny App
ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.
Maintained by Pacome Prompsy. Last updated 5 months ago.
shinyappssoftwaresinglecellchipseqatacseqmethylseqclassificationclusteringepigeneticsprincipalcomponentannotationbatcheffectmultiplecomparisonnormalizationpathwayspreprocessingqualitycontrolreportwritingvisualizationgenesetenrichmentdifferentialpeakcallingepigenomicsshinysingle-cellcpp
14 stars 5.83 score 16 scriptsbioc
sangeranalyseR:sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.
Maintained by Kuan-Hao Chao. Last updated 30 days ago.
geneticsalignmentsequencingsangerseqpreprocessingqualitycontrolvisualizationgui
5.76 score 46 scriptsbioc
iSEEindex:iSEE extension for a landing page to a custom collection of data sets
This package provides an interface to any collection of data sets within a single iSEE web-application. The main functionality of this package is to define a custom landing page allowing app maintainers to list a custom collection of data sets that users can selected from and directly load objects into an iSEE web-application.
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
softwareinfrastructurebioconductorhacktoberfest
2 stars 5.65 score 8 scripts
christophsax
seasonalview:Graphical User Interface for Seasonal Adjustment
A graphical user interface to the 'seasonal' package and 'X-13ARIMA-SEATS', the U.S. Census Bureau's seasonal adjustment software.
Maintained by Christoph Sax. Last updated 5 months ago.
seasonal-adjustmentshinytime-series
22 stars 5.65 score 105 scripts
bioc
iSEEhub:iSEE for the Bioconductor ExperimentHub
This package defines a custom landing page for an iSEE app interfacing with the Bioconductor ExperimentHub. The landing page allows users to browse the ExperimentHub, select a data set, download and cache it, and import it directly into a Bioconductor iSEE app.
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
dataimportimmunooncology infrastructureshinyappssinglecellsoftwarebioconductorbioconductor-packagehacktoberfestisee
3 stars 5.56 score 4 scripts
mponce0
covid19.analytics:Load and Analyze Live Data from the COVID-19 Pandemic
Load and analyze updated time series worldwide data of reported cases for the Novel Coronavirus Disease (COVID-19) from different sources, including the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE) data repository <https://github.com/CSSEGISandData/COVID-19>, "Our World in Data" <https://github.com/owid/> among several others. The datasets reporting the COVID-19 cases are available in two main modalities, as a time series sequences and aggregated data for the last day with greater spatial resolution. Several analysis, visualization and modelling functions are available in the package that will allow the user to compute and visualize total number of cases, total number of changes and growth rate globally or for an specific geographical location, while at the same time generating models using these trends; generate interactive visualizations and generate Susceptible-Infected-Recovered (SIR) model for the disease spread.
Maintained by Marcelo Ponce. Last updated 3 years ago.
covid19covid19-datancov2019sars-cov-2
33 stars 5.52 score 20 scriptsbioc
cbpManager:Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics
This R package provides an R Shiny application that enables the user to generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. Create cancer studies and edit its metadata. Upload mutation data of a patient that will be concatenated to the data_mutation_extended.txt file of the study. Create and edit clinical patient data, sample data, and timeline data. Create custom timeline tracks for patients.
Maintained by Arsenij Ustjanzew. Last updated 5 months ago.
immunooncologydataimportdatarepresentationguithirdpartyclientpreprocessingvisualizationcancer-genomicscbioportalclinical-datafilegeneratormutation-datapatient-data
8 stars 5.51 score 1 scriptsbioc
cytoviewer:An interactive multi-channel image viewer for R
This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image downloads.
Maintained by Lasse Meyer. Last updated 5 months ago.
immunooncologysoftwaresinglecellonechanneltwochannelmultichannelspatialdataimportbioconductorimagingshinyvisualization
7 stars 5.50 score 15 scripts
paulgovan
BayesianNetwork:Bayesian Network Modeling and Analysis
A "Shiny"" web application for creating interactive Bayesian Network models, learning the structure and parameters of Bayesian networks, and utilities for classic network analysis.
Maintained by Paul Govan. Last updated 4 months ago.
bayesian-networkslearning-algorithmnetwork-measures
121 stars 5.48 score 1 scripts
el-meyer
airship:Visualization of Simulated Datasets with Multiple Simulation Input Dimensions
Plots simulation results of clinical trials. Its main feature is allowing users to simultaneously investigate the impact of several simulation input dimensions through dynamic filtering of the simulation results. A more detailed description of the app can be found in Meyer et al. <DOI:10.1016/j.softx.2023.101347> or the vignettes on 'GitHub'.
Maintained by Elias Laurin Meyer. Last updated 4 months ago.
clinical-trialsggplot2interactiveinteractive-visualizationssimulationvisualization
3 stars 5.48 score 2 scripts
confoobio
GMSE:Generalised Management Strategy Evaluation Simulator
Integrates game theory and ecological theory to construct social-ecological models that simulate the management of populations and stakeholder actions. These models build off of a previously developed management strategy evaluation (MSE) framework to simulate all aspects of management: population dynamics, manager observation of populations, manager decision making, and stakeholder responses to management decisions. The newly developed generalised management strategy evaluation (GMSE) framework uses genetic algorithms to mimic the decision-making process of managers and stakeholders under conditions of change, uncertainty, and conflict. Simulations can be run using gmse(), gmse_apply(), and gmse_gui() functions.
Maintained by A. Bradley Duthie. Last updated 3 years ago.
adaptive-managementagricultural-modellingconflictconflict-resolutionconservationecological-modellingecological-modelsecologyfood-securitygame-theorygenetic-algorithmgenetic-algorithmsmanagement-decisionsmanagement-strategy-evaluationpopulation-modelsimulationwildlife-management
10 stars 5.43 score 178 scripts
zheng206
ComBatFamQC:Comprehensive Batch Effect Diagnostics and Harmonization
Provides a comprehensive framework for batch effect diagnostics, harmonization, and post-harmonization downstream analysis. Features include interactive visualization tools, robust statistical tests, and a range of harmonization techniques. Additionally, 'ComBatFamQC' enables the creation of life-span age trend plots with estimated age-adjusted centiles and facilitates the generation of covariate-corrected residuals for analytical purposes. Methods for harmonization are based on approaches described in Johnson et al., (2007) <doi:10.1093/biostatistics/kxj037>, Beer et al., (2020) <doi:10.1016/j.neuroimage.2020.117129>, Pomponio et al., (2020) <doi:10.1016/j.neuroimage.2019.116450>, and Chen et al., (2021) <doi:10.1002/hbm.25688>.
Maintained by Zheng Ren. Last updated 9 days ago.
diagnostic-toolharmonizationrshinyapp
2 stars 5.41 score 16 scripts
kgjerde
corporaexplorer:A 'Shiny' App for Exploration of Text Collections
Facilitates dynamic exploration of text collections through an intuitive graphical user interface and the power of regular expressions. The package contains 1) a helper function to convert a data frame to a 'corporaexplorerobject' and 2) a 'Shiny' app for fast and flexible exploration of a 'corporaexplorerobject'. The package also includes demo apps with which one can explore Jane Austen's novels and the State of the Union Addresses (data from the 'janeaustenr' and 'sotu' packages respectively).
Maintained by Kristian Lundby Gjerde. Last updated 7 months ago.
corporacorpusshinytext-analysis
65 stars 5.39 score 38 scriptsbioc
iSEEde:iSEE extension for panels related to differential expression analysis
This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
softwareinfrastructuredifferentialexpressionbioconductorhacktoberfestiseeu
1 stars 5.38 score 15 scriptsbioc
iSEEhex:iSEE extension for summarising data points in hexagonal bins
This package provides panels summarising data points in hexagonal bins for `iSEE`. It is part of `iSEEu`, the iSEE universe of panels that extend the `iSEE` package.
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
softwareinfrastructurebioconductoriseeushiny-r
5.38 score 7 scripts 2 dependentsbioc
MsQuality:MsQuality - Quality metric calculation from Spectra and MsExperiment objects
The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.
Maintained by Thomas Naake. Last updated 2 months ago.
metabolomicsproteomicsmassspectrometryqualitycontrolmass-spectrometryqc
7 stars 5.32 score 2 scripts
yulab-smu
shinyTempSignal:Explore Temporal and Other Phylogenetic Signals
Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels. The method was extended to support exploring other phylogenetic signals under strict and relaxed models.
Maintained by Guangchuang Yu. Last updated 1 years ago.
molecular-clockphylogeneticsshiny-app
9 stars 5.26 score 7 scripts
pydemull
activAnalyzer:A 'Shiny' App to Analyze Accelerometer-Measured Daily Physical Behavior Data
A tool to analyse 'ActiGraph' accelerometer data and to implement the use of the PROactive Physical Activity in COPD (chronic obstructive pulmonary disease) instruments. Once analysis is completed, the app allows to export results to .csv files and to generate a report of the measurement. All the configured inputs relevant for interpreting the results are recorded in the report. In addition to the existing 'R' packages that are fully integrated with the app, the app uses some functions from the 'actigraph.sleepr' package developed by Petkova (2021) <https://github.com/dipetkov/actigraph.sleepr/>.
Maintained by Pierre-Yves de Müllenheim. Last updated 11 days ago.
accelerometeractigraphappmonitorshiny
5 stars 5.24 score 8 scripts
lamate
mlr3shiny:Machine Learning in 'shiny' with 'mlr3'
A web-based graphical user interface to provide the basic steps of a machine learning workflow. It uses the functionalities of the 'mlr3' framework.
Maintained by Laurens Tetzlaff. Last updated 10 months ago.
data-scienceintroduction-to-machine-learningmachine-learningmlr3shinysupervised-learning
28 stars 5.23 score 1 scriptsbioc
gDR:Umbrella package for R packages in the gDR suite
Package is a part of the gDR suite. It reexports functions from other packages in the gDR suite that contain critical processing functions and utilities. The vignette walks through the full processing pipeline for drug response analyses that the gDR suite offers.
Maintained by Arkadiusz Gladki. Last updated 5 months ago.
1 stars 5.20 score 7 scripts
biodosetools-team
biodosetools:An R Shiny Application for Biological Dosimetry
A tool to perform all different statistical tests and calculations needed by Biological Dosimetry Laboratories. Detailed documentation is available in <https://biodosetools-team.github.io/documentation/> and the paper by Hernández et al. (2023) <doi:10.1080/09553002.2023.2176564>.
Maintained by Alfredo Hernández. Last updated 4 months ago.
biological-datadosimetryshiny-app
5 stars 5.20 score 16 scripts
scollinselliott
lakhesis:Consensus Seriation for Binary Data
Determining consensus seriations for binary incidence matrices, using a two-step process of Procrustes-fit correspondence analysis for heuristic selection of partial seriations and iterative regression to establish a single consensus. Contains the Lakhesis Calculator, a graphical platform for identifying seriated sequences. Collins-Elliott (2024) <https://volweb.utk.edu/~scolli46/sceLakhesis.pdf>.
Maintained by Stephen A. Collins-Elliott. Last updated 4 months ago.
archaeologybinary-datacorrespondence-analysisecologyseriation
5 stars 5.18 score 2 scripts
massimoaria
tall:Text Analysis for All
An R 'shiny' app designed for diverse text analysis tasks, offering a wide range of methodologies tailored to Natural Language Processing (NLP) needs. It is a versatile, general-purpose tool for analyzing textual data. 'tall' features a comprehensive workflow, including data cleaning, preprocessing, statistical analysis, and visualization, all integrated for effective text analysis.
Maintained by Massimo Aria. Last updated 13 days ago.
r-shinytext-analysis-and-sentiment-analysistext-classificationtext-miningtextual-analysiscpp
15 stars 5.15 score
promidat
loadeR:Load Data for Analysis System
Provides a framework to load text and excel files through a 'shiny' graphical interface. It allows renaming, transforming, ordering and removing variables. It includes basic exploratory methods such as the mean, median, mode, normality test, histogram and correlation.
Maintained by Oldemar Rodriguez. Last updated 2 years ago.
5.09 score 275 scripts 3 dependents
openpharma
elaborator:A 'shiny' Application for Exploring Laboratory Data
A novel concept for generating knowledge and gaining insights into laboratory data. You will be able to efficiently and easily explore your laboratory data from different perspectives. Janitza, S., Majumder, M., Mendolia, F., Jeske, S., & Kulmann, H. (2021) <doi:10.1007/s43441-021-00318-4>.
Maintained by Bodo Kirsch. Last updated 13 hours ago.
clinical-trialsdata-insightslaboratory-dataqualitative-trend-analysisreference-valuesshiny-appsvisualization
8 stars 5.08 scorebioc
chevreulShiny:Tools for managing SingleCellExperiment objects as projects
Tools for managing SingleCellExperiment objects as projects. Includes functions for analysis and visualization of single-cell data. Also included is a shiny app for visualization of pre-processed scRNA data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.
Maintained by Kevin Stachelek. Last updated 29 days ago.
coveragernaseqsequencingvisualizationgeneexpressiontranscriptionsinglecelltranscriptomicsnormalizationpreprocessingqualitycontroldimensionreductiondataimport
5.08 score
celehs
phecodemap:Visualization for Phecode Mapping with ICD-9 and ICD-10-cm Codes
Phecodemap builds a shiny app to visualize the hierarchy of Phecode Mapping with ICD. The same Phecode hierarchy is displayed in two ways: as a sunburst plot and as a tree.
Maintained by Parse Health. Last updated 1 years ago.
3 stars 5.07 score 13 scripts
lidiamandre
ReturnCurves:Estimation of Return Curves
Estimates the p-probability return curve proposed by Murphy-Barltrop et al. (2023) <doi:10.1002/env.2797>. Implements pointwise and smooth estimation of the angular dependence function introduced by Wadsworth and Tawn (2013) <doi:10.3150/12-BEJ471>.
Maintained by Lídia André. Last updated 2 months ago.
1 stars 5.06 score 19 scripts
waynegitshell
GWSDAT:GroundWater Spatiotemporal Data Analysis Tool (GWSDAT)
Shiny application for the analysis of groundwater monitoring data, designed to work with simple time-series data for solute concentration and ground water elevation, but can also plot non-aqueous phase liquid (NAPL) thickness if required. Also provides the import of a site basemap in GIS shapefile format.
Maintained by Wayne Jones. Last updated 1 years ago.
contamination-detectiongroundwater-flowplumeshinyspatio-temporal-analysis
32 stars 5.02 score 11 scriptsbioc
InterCellar:InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics
InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore clusters, genes and functions. Finally, based on functional annotation from Gene Ontology and pathway databases, InterCellar implements data-driven analyses to investigate cell-cell communication in one or multiple conditions.
Maintained by Marta Interlandi. Last updated 5 months ago.
softwaresinglecellvisualizationgotranscriptomics
9 stars 4.95 score 7 scriptsbioc
iSEEpathways:iSEE extension for panels related to pathway analysis
This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
softwareinfrastructuredifferentialexpressiongeneexpressionguivisualizationpathwaysgenesetenrichmentgoshinyappsbioconductorhacktoberfestiseeiseeu
1 stars 4.95 score 10 scripts
okanbulut
eirm:Explanatory Item Response Modeling for Dichotomous and Polytomous Items
Analysis of dichotomous and polytomous response data using the explanatory item response modeling framework, as described in Bulut, Gorgun, & Yildirim-Erbasli (2021) <doi:10.3390/psych3030023>, Stanke & Bulut (2019) <doi:10.21449/ijate.515085>, and De Boeck & Wilson (2004) <doi:10.1007/978-1-4757-3990-9>. Generalized linear mixed modeling is used for estimating the effects of item-related and person-related variables on dichotomous and polytomous item responses.
Maintained by Okan Bulut. Last updated 2 years ago.
8 stars 4.90 score
dylanpieper
batchLLM:Batch Process LLM Text Completions Using a Data Frame
Batch process large language model (LLM) text completions using data frame rows, with support for OpenAI's 'GPT' (<https://chat.openai.com>), Anthropic's 'Claude' (<https://claude.ai>), and Google's 'Gemini' (<https://gemini.google.com>). Includes features such as local storage, metadata logging, API rate limiting delays, and a 'shiny' app addin.
Maintained by Dylan Pieper. Last updated 2 months ago.
11 stars 4.85 score 6 scriptspaulgovan
eAnalytics:Dynamic Web-Based Analytics for the Energy Industry
A 'Shiny' web application for energy industry analytics. Take an overview of the industry, measure Key Performance Indicators, identify changes in the industry over time, and discover new relationships in the data.
Maintained by Paul Govan. Last updated 7 months ago.
analyticsenergyshinyshinydashboardvisualization
34 stars 4.83 score 1 scripts
arsilva87
soilphysics:Soil Physical Analysis
Basic and model-based soil physical analyses.
Maintained by Anderson Rodrigo da Silva. Last updated 3 years ago.
11 stars 4.83 score 12 scripts
seewe
dataCompare:A 'shiny' App to Compare Two Data Frames
A tool developed with the 'Golem' framework which provides an easier way to check cells differences between two data frames. The user provides two data frames for comparison, selects IDs variables identifying each row of input data, then clicks a button to perform the comparison. Several 'R' package functions are used to describe the data and perform the comparison in the server of the application. The main ones are comparedf() from 'arsenal' and skim() from 'skimr'. For more details see the description of comparedf() from the 'arsenal' package and that of skim() from the 'skimr' package.
Maintained by Sergio Ewane Ebouele. Last updated 3 months ago.
2 stars 4.78 score 4 scriptsbioc
clevRvis:Visualization Techniques for Clonal Evolution
clevRvis provides a set of visualization techniques for clonal evolution. These include shark plots, dolphin plots and plaice plots. Algorithms for time point interpolation as well as therapy effect estimation are provided. Phylogeny-aware color coding is implemented. A shiny-app for generating plots interactively is additionally provided.
Maintained by Sarah Sandmann. Last updated 5 months ago.
softwareshinyappsvisualization
6 stars 4.78 score 2 scriptsbioc
wpm:Well Plate Maker
The Well-Plate Maker (WPM) is a shiny application deployed as an R package. Functions for a command-line/script use are also available. The WPM allows users to generate well plate maps to carry out their experiments while improving the handling of batch effects. In particular, it helps controlling the "plate effect" thanks to its ability to randomize samples over multiple well plates. The algorithm for placing the samples is inspired by the backtracking algorithm: the samples are placed at random while respecting specific spatial constraints.
Maintained by Helene Borges. Last updated 5 months ago.
guiproteomicsmassspectrometrybatcheffectexperimentaldesign
6 stars 4.78 score 7 scriptsbioc
gINTomics:Multi-Omics data integration
gINTomics is an R package for Multi-Omics data integration and visualization. gINTomics is designed to detect the association between the expression of a target and of its regulators, taking into account also their genomics modifications such as Copy Number Variations (CNV) and methylation. What is more, gINTomics allows integration results visualization via a Shiny-based interactive app.
Maintained by Angelo Velle. Last updated 5 months ago.
geneexpressionrnaseqmicroarrayvisualizationcopynumbervariationgenetargetquarto
3 stars 4.78 score 3 scriptsbioc
scanMiRApp:scanMiR shiny application
A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.
Maintained by Pierre-Luc Germain. Last updated 5 months ago.
mirnasequencematchingguishinyapps
4.76 score 19 scriptsbioc
MatrixQCvis:Shiny-based interactive data-quality exploration for omics data
Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the MatrixQCvis package, which provides shiny-based interactive visualization of data quality metrics at the per-sample and per-feature level. It is broadly applicable to quantitative omics data types that come in matrix-like format (features x samples). It enables the detection of low-quality samples, drifts, outliers and batch effects in data sets. Visualizations include amongst others bar- and violin plots of the (count/intensity) values, mean vs standard deviation plots, MA plots, empirical cumulative distribution function (ECDF) plots, visualizations of the distances between samples, and multiple types of dimension reduction plots. Furthermore, MatrixQCvis allows for differential expression analysis based on the limma (moderated t-tests) and proDA (Wald tests) packages. MatrixQCvis builds upon the popular Bioconductor SummarizedExperiment S4 class and enables thus the facile integration into existing workflows. The package is especially tailored towards metabolomics and proteomics mass spectrometry data, but also allows to assess the data quality of other data types that can be represented in a SummarizedExperiment object.
Maintained by Thomas Naake. Last updated 5 months ago.
visualizationshinyappsguiqualitycontroldimensionreductionmetabolomicsproteomicstranscriptomics
4.74 score 4 scripts
mreginato
monographaR:Taxonomic Monographs Tools
Contains functions intended to facilitate the production of plant taxonomic monographs. The package includes functions to convert tables into taxonomic descriptions, lists of collectors, examined specimens, identification keys (dichotomous and interactive), and can generate a monograph skeleton. Additionally, wrapper functions to batch the production of phenology histograms and distributional and diversity maps are also available.
Maintained by Marcelo Reginato. Last updated 1 years ago.
3 stars 4.73 score 18 scripts
garthtarr
mplot:Graphical Model Stability and Variable Selection Procedures
Model stability and variable inclusion plots [Mueller and Welsh (2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller (2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al. (2008, <doi:10.1214/07-AOS517>); Jiang et al. (2009, <doi:10.1016/j.spl.2008.10.014>)] for linear and generalised linear models.
Maintained by Garth Tarr. Last updated 4 years ago.
12 stars 4.70 score 42 scriptsbioc
GNOSIS:Genomics explorer using statistical and survival analysis in R
GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.
Maintained by Lydia King. Last updated 5 months ago.
5 stars 4.70 score 2 scripts
cygei
mixtree:A Statistical Framework for Comparing Sets of Trees
Apply hypothesis testing methods to assess differences between sets of trees.
Maintained by Cyril Geismar. Last updated 1 months ago.
4.70 score
duolajiang
RCTrep:Validation of Estimates of Treatment Effects in Observational Data
Validates estimates of (conditional) average treatment effects obtained using observational data by a) making it easy to obtain and visualize estimates derived using a large variety of methods (G-computation, inverse propensity score weighting, etc.), and b) ensuring that estimates are easily compared to a gold standard (i.e., estimates derived from randomized controlled trials). 'RCTrep' offers a generic protocol for treatment effect validation based on four simple steps, namely, set-selection, estimation, diagnosis, and validation. 'RCTrep' provides a simple dashboard to review the obtained results. The validation approach is introduced by Shen, L., Geleijnse, G. and Kaptein, M. (2023) <doi:10.21203/rs.3.rs-2559287/v1>.
Maintained by Lingjie Shen. Last updated 2 years ago.
8 stars 4.68 score 12 scripts
trackerproject
trackeRapp:Interface for the Analysis of Running, Cycling and Swimming Data from GPS-Enabled Tracking Devices
Provides an integrated user interface and workflow for the analysis of running, cycling and swimming data from GPS-enabled tracking devices through the 'trackeR' <https://CRAN.R-project.org/package=trackeR> R package.
Maintained by Ioannis Kosmidis. Last updated 3 years ago.
data-visualizationshinysports-appweb-appweb-development
32 stars 4.68 score 2 scripts
ropensci
MtreeRing:A Shiny Application for Automatic Measurements of Tree-Ring Widths on Digital Images
Use morphological image processing and edge detection algorithms to automatically measure tree ring widths on digital images. Users can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. The package provides a Shiny-based application, allowing R beginners to easily analyze tree ring images and export ring-width series in standard file formats.
Maintained by Jingning Shi. Last updated 9 months ago.
dendrochronologyforestforestryshiny-appsshinyapptree-ring-widthtree-rings
33 stars 4.66 score 14 scripts
avrodrigues
naturaList:Classify Occurrences by Confidence Levels in the Species ID
Classify occurrence records based on confidence levels of species identification. In addition, implement tools to filter occurrences inside grid cells and to manually check for possibles errors with an interactive shiny application.
Maintained by Arthur Vinicius Rodrigues. Last updated 1 years ago.
4.66 score 23 scripts
osimon81
SqueakR:An Experiment Interface for 'DeepSqueak' Bioacoustics Research
Data processing and visualizations for rodent vocalizations exported from 'DeepSqueak'. These functions are compatible with the 'SqueakR' Shiny Dashboard, which can be used to visualize experimental results and analyses.
Maintained by Simon Ogundare. Last updated 3 years ago.
9 stars 4.65 score 5 scriptsbioc
iSEEfier:Streamlining the creation of initial states for starting an iSEE instance
iSEEfier provides a set of functionality to quickly and intuitively create, inspect, and combine initial configuration objects. These can be conveniently passed in a straightforward manner to the function call to launch iSEE() with the specified configuration. This package currently works seamlessly with the sets of panels provided by the iSEE and iSEEu packages, but can be extended to accommodate the usage of any custom panel (e.g. from iSEEde, iSEEpathways, or any panel developed independently by the user).
Maintained by Najla Abassi. Last updated 5 months ago.
cellbasedassaysclusteringdimensionreductionfeatureextractionguigeneexpressionimmunooncologyshinyappssinglecellsoftwaretranscriptiontranscriptomicsvisualization
4.60 score 2 scriptsbioc
OGRE:Calculate, visualize and analyse overlap between genomic regions
OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs, or reads from sequencing experiments. Key numbers help analyse the extend of overlaps which can also be visualized at a genomic level.
Maintained by Sven Berres. Last updated 5 months ago.
softwareworkflowstepbiologicalquestionannotationmetagenomicsvisualizationsequencing
2 stars 4.60 score 4 scriptsbioc
ComPrAn:Complexome Profiling Analysis package
This package is for analysis of SILAC labeled complexome profiling data. It uses peptide table in tab-delimited format as an input and produces ready-to-use tables and plots.
Maintained by Petra Palenikova. Last updated 5 months ago.
massspectrometryproteomicsvisualization
4.48 score 5 scripts
javierdelahoz
LDAShiny:User-Friendly Interface for Review of Scientific Literature
Contains the development of a tool that provides a web-based graphical user interface (GUI) to perform a review of the scientific literature under the Bayesian approach of Latent Dirichlet Allocation (LDA)and machine learning algorithms. The application methodology is framed by the well known procedures in topic modelling on how to clean and process data. Contains methods described by Blei, David M., Andrew Y. Ng, and Michael I. Jordan (2003) <https://jmlr.org/papers/volume3/blei03a/blei03a.pdf> Allocation"; Thomas L. Griffiths and Mark Steyvers (2004) <doi:10.1073/pnas.0307752101> ; Xiong Hui, et al (2019) <doi:10.1016/j.cie.2019.06.010>.
Maintained by Javier De La Hoz Maestre. Last updated 4 years ago.
3 stars 4.48 score 3 scripts
chaoliu-cl
textAnnotatoR:Interactive Text Annotation Tool with 'shiny' GUI
A comprehensive text annotation tool built with 'shiny'. Provides an interactive graphical user interface for coding text documents, managing code hierarchies, creating memos, and analyzing coding patterns. Features include code co-occurrence analysis, visualization of coding patterns, comparison of multiple coding sets, and export capabilities. Supports collaborative qualitative research through standardized annotation formats and analysis tools.
Maintained by Chao Liu. Last updated 8 days ago.
4.48 score 5 scripts
sfilges
umiAnalyzer:Tools for Analyzing Sequencing Data with Unique Molecular Identifiers
Tools for analyzing sequencing data containing unique molecular identifiers generated by 'UMIErrorCorrect' (<https://github.com/stahlberggroup/umierrorcorrect>).
Maintained by Stefan Filges. Last updated 3 years ago.
targeted-sequencingunique-molecular-identifiersvariant-analysis
4.46 score 58 scriptsbioc
ToxicoGx:Analysis of Large-Scale Toxico-Genomic Data
Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftware
4.36 score 23 scriptsbioc
PDATK:Pancreatic Ductal Adenocarcinoma Tool-Kit
Pancreatic ductal adenocarcinoma (PDA) has a relatively poor prognosis and is one of the most lethal cancers. Molecular classification of gene expression profiles holds the potential to identify meaningful subtypes which can inform therapeutic strategy in the clinical setting. The Pancreatic Cancer Adenocarcinoma Tool-Kit (PDATK) provides an S4 class-based interface for performing unsupervised subtype discovery, cross-cohort meta-clustering, gene-expression-based classification, and subsequent survival analysis to identify prognostically useful subtypes in pancreatic cancer and beyond. Two novel methods, Consensus Subtypes in Pancreatic Cancer (CSPC) and Pancreatic Cancer Overall Survival Predictor (PCOSP) are included for consensus-based meta-clustering and overall-survival prediction, respectively. Additionally, four published subtype classifiers and three published prognostic gene signatures are included to allow users to easily recreate published results, apply existing classifiers to new data, and benchmark the relative performance of new methods. The use of existing Bioconductor classes as input to all PDATK classes and methods enables integration with existing Bioconductor datasets, including the 21 pancreatic cancer patient cohorts available in the MetaGxPancreas data package. PDATK has been used to replicate results from Sandhu et al (2019) [https://doi.org/10.1200/cci.18.00102] and an additional paper is in the works using CSPC to validate subtypes from the included published classifiers, both of which use the data available in MetaGxPancreas. The inclusion of subtype centroids and prognostic gene signatures from these and other publications will enable researchers and clinicians to classify novel patient gene expression data, allowing the direct clinical application of the classifiers included in PDATK. Overall, PDATK provides a rich set of tools to identify and validate useful prognostic and molecular subtypes based on gene-expression data, benchmark new classifiers against existing ones, and apply discovered classifiers on novel patient data to inform clinical decision making.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationsurvivalclusteringgeneprediction
1 stars 4.31 score 17 scripts
loosolab
wilson:Web-Based Interactive Omics Visualization
Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data. This package utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
Maintained by Hendrik Schultheis. Last updated 4 years ago.
2 stars 4.30 score 7 scriptsbioc
Ularcirc:Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools for splicing analysis. Users can assess backsplice junctions and forward canonical junctions.
Maintained by David Humphreys. Last updated 5 months ago.
datarepresentationvisualizationgeneticssequencingannotationcoveragealternativesplicingdifferentialsplicing
4.30 score 4 scripts
jiangyouxiang
TestAnaAPP:A 'shiny' App for Test Analysis and Visualization
This application provides exploratory and confirmatory factor analysis, classical test theory, unidimensional and multidimensional item response theory, and continuous item response model analysis, through the 'shiny' interactive interface. In addition, it offers rich functionalities for visualizing and downloading results. Users can download figures, tables, and analysis reports via the interactive interface.
Maintained by Youxiang Jiang. Last updated 4 months ago.
4 stars 4.30 score 2 scriptsbioc
protGear:Protein Micro Array Data Management and Interactive Visualization
A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.
Maintained by Kennedy Mwai. Last updated 5 months ago.
microarrayonechannelpreprocessingbiomedicalinformaticsproteomicsbatcheffectnormalizationbayesianclusteringregressionsystemsbiologyimmunooncologybackground-correctionmicroarray-datanormalisationproteomics-datashinyshinydashboard
1 stars 4.30 score 6 scripts
uofuepibio
epiworldRShiny:A 'shiny' Wrapper of the R Package 'epiworldR'
R 'shiny' web apps for epidemiological Agent-Based Models. It provides a user-friendly interface to the Agent-Based Modeling (ABM) R package 'epiworldR' (Meyer et al., 2023) <DOI:10.21105/joss.05781>. Some of the main features of the package include the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Recovered (SIR), and Susceptible-Exposed-Infected-Recovered (SEIR) models. 'epiworldRShiny' provides a web-based user interface for running various epidemiological ABMs, simulating interventions, and visualizing results interactively.
Maintained by Derek Meyer. Last updated 1 days ago.
abmagent-based-modelingcovid-19epidemic-simulationsepidemiologynetscinetwork-analysisshinyappsshinydashboardsimulation-modeling
1 stars 4.18 score 4 scripts
johannes-titz
cofad:Contrast Analyses for Factorial Designs
Contrast analysis for factorial designs provides an alternative to the traditional ANOVA approach, offering the distinct advantage of testing targeted hypotheses. The foundation of this package is primarily rooted in the works of Rosenthal, Rosnow, and Rubin (2000, ISBN: 978-0521659802) as well as Sedlmeier and Renkewitz (2018, ISBN: 978-3868943214).
Maintained by Johannes Titz. Last updated 20 days ago.
2 stars 4.15 score 7 scripts
miracum
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 2 months ago.
2 stars 4.15 score 10 scripts
arliph
SPARTAAS:Statistical Pattern Recognition and daTing using Archaeological Artefacts assemblageS
Statistical pattern recognition and dating using archaeological artefacts assemblages. Package of statistical tools for archaeology. hclustcompro(perioclust): Bellanger Lise, Coulon Arthur, Husi Philibrary(SPARTlippe (2021, ISBN:978-3-030-60103-4). mapclust: Bellanger Lise, Coulon Arthur, Husi Philippe (2021) <doi:10.1016/j.jas.2021.105431>. seriograph: Desachy Bruno (2004) <doi:10.3406/pica.2004.2396>. cerardat: Bellanger Lise, Husi Philippe (2012) <doi:10.1016/j.jas.2011.06.031>.
Maintained by Arthur Coulon. Last updated 10 months ago.
6 stars 4.14 score 46 scripts
danielebizzarri
MiMIR:Metabolomics-Based Models for Imputing Risk
Provides an intuitive framework for ad-hoc statistical analysis of 1H-NMR metabolomics by Nightingale Health. It allows to easily explore new metabolomics measurements assayed by Nightingale Health, comparing the distributions with a large Consortium (BBMRI-nl); project previously published metabolic scores [<doi:10.1016/j.ebiom.2021.103764>, <doi:10.1161/CIRCGEN.119.002610>, <doi:10.1038/s41467-019-11311-9>, <doi:10.7554/eLife.63033>, <doi:10.1161/CIRCULATIONAHA.114.013116>, <doi:10.1007/s00125-019-05001-w>]; and calibrate the metabolic surrogate values to a desired dataset.
Maintained by Daniele Bizzarri. Last updated 2 years ago.
binary-risk-factorsbiomarkerslinear-regressionmetabolitesmetabolomicsnightingale-metabolomicsrisk-factor-modelsrisk-factorssurrogate-models
8 stars 4.11 score 32 scripts
pedroliman
arena2r:Plots, Summary Statistics and Tools for Arena Simulation Users
Reads Arena <https://www.arenasimulation.com/> CSV output files and generates nice tables and plots. The package contains a 'Shiny' App that can be used to interactively visualize Arena's results.
Maintained by Pedro Nascimento de Lima. Last updated 6 years ago.
4.02 score 21 scripts
amderoos
deBif:Bifurcation Analysis of Ordinary Differential Equation Systems
Shiny application that performs bifurcation and phaseplane analysis of systems of ordinary differential equations. The package allows for computation of equilibrium curves as a function of a single free parameter, detection of transcritical, saddle-node and hopf bifurcation points along these curves, and computation of curves representing these transcritical, saddle-node and hopf bifurcation points as a function of two free parameters. The shiny-based GUI allows visualization of the results in both 2D- and 3D-plots. The implemented methods for solution localisation and curve continuation are based on the book "Elements of applied bifurcation theory" (Kuznetsov, Y. A., 1995; ISBN: 0-387-94418-4).
Maintained by Andre M. de Roos. Last updated 1 months ago.
4.00 score 3 scriptsbioc
microbiomeExplorer:Microbiome Exploration App
The MicrobiomeExplorer R package is designed to facilitate the analysis and visualization of marker-gene survey feature data. It allows a user to perform and visualize typical microbiome analytical workflows either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows the application enables automated analysis report generation.
Maintained by Janina Reeder. Last updated 5 months ago.
classificationclusteringgeneticvariabilitydifferentialexpressionmicrobiomemetagenomicsnormalizationvisualizationmultiplecomparisonsequencingsoftwareimmunooncology
4.00 score 8 scriptsbioc
Doscheda:A DownStream Chemo-Proteomics Analysis Pipeline
Doscheda focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass Spectrometry data. The package provides a shiny application to run the pipeline, several visualisations and a downloadable report of an experiment.
Maintained by Bruno Contrino. Last updated 5 months ago.
proteomicsnormalizationpreprocessingmassspectrometryqualitycontroldataimportregression
4.00 score 2 scriptscelehs
kesernetwork:Visualization of the KESER Network
A shiny app to visualize the knowledge networks for the code concepts. Using co-occurrence matrices of EHR codes from Veterans Affairs (VA) and Massachusetts General Brigham (MGB), the knowledge extraction via sparse embedding regression (KESER) algorithm was used to construct knowledge networks for the code concepts. Background and details about the method can be found at Chuan et al. (2021) <doi:10.1038/s41746-021-00519-z>.
Maintained by Su-Chun Cheng. Last updated 2 years ago.
1 stars 4.00 score 7 scripts
fentouxungui
SeuratExplorer:An 'Shiny' App for Exploring scRNA-seq Data Processed in 'Seurat'
A simple, one-command package which runs an interactive dashboard capable of common visualizations for single cell RNA-seq. 'SeuratExplorer' requires a processed 'Seurat' object, which is saved as 'rds' or 'qs2' file.
Maintained by Yongchao Zhang. Last updated 18 hours ago.
3.98 score
mmollina
viewpoly:A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species
Provides a graphical user interface to integrate, visualize and explore results from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid species. The app is meant for interactive use and allows users to optionally upload different sources of information, including gene annotation and alignment files, enabling the exploitation and search for candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly', 'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.
Maintained by Cristiane Taniguti. Last updated 1 months ago.
4 stars 3.90 score 2 scripts
magnusdv
KLINK:Kinship Analysis with Linked Markers
A 'shiny' application for forensic kinship testing, based on the 'pedsuite' R packages. 'KLINK' is closely aligned with the (non-R) software 'Familias' and 'FamLink', but offers several unique features, including visualisations and automated report generation. The calculation of likelihood ratios supports pairs of linked markers, and all common mutation models.
Maintained by Magnus Dehli Vigeland. Last updated 21 days ago.
forensic-geneticskinship-testingpedsuiteshiny
1 stars 3.88 score 5 scripts
swfsc
CruzPlot:Plot Shipboard DAS Data
A utility program oriented to create maps, plot data, and do basic data summaries of DAS data files. These files are typically, but do not have to be DAS <https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-305.PDF> data produced by the Southwest Fisheries Science Center (SWFSC) program 'WinCruz'.
Maintained by Sam Woodman. Last updated 6 months ago.
2 stars 3.85 score 2 scripts
medianasoft
MedianaDesigner:Power and Sample Size Calculations for Clinical Trials
Efficient simulation-based power and sample size calculations are supported for a broad class of late-stage clinical trials. The following modules are included in the package: Adaptive designs with data-driven sample size or event count re-estimation, Adaptive designs with data-driven treatment selection, Adaptive designs with data-driven population selection, Optimal selection of a futility stopping rule, Event prediction in event-driven trials, Adaptive trials with response-adaptive randomization (experimental module), Traditional trials with multiple objectives (experimental module). Traditional trials with cluster-randomized designs (experimental module).
Maintained by Alex Dmitrienko. Last updated 2 years ago.
20 stars 3.79 score 31 scriptsbioc
famat:Functional analysis of metabolic and transcriptomic data
Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: - Pathways containing some of the user's genes and metabolites (obtained using a pathway enrichment analysis). - Direct interactions between user's elements inside pathways. - Information about elements (their identifiers and descriptions). - Go terms enrichment analysis performed on user's genes. The Shiny app is composed of: - information about genes, metabolites, and direct interactions between them inside pathways. - an heatmap showing which elements from the list are in pathways (pathways are structured in hierarchies). - hierarchies of enriched go terms using Molecular Function and Biological Process.
Maintained by Mathieu Charles. Last updated 5 months ago.
functionalpredictiongenesetenrichmentpathwaysgoreactomekeggcompoundgene-ontologygenesshiny
1 stars 3.78 score 2 scripts
jo-theo
shinySbm:'shiny' Application to Use the Stochastic Block Model
A 'shiny' interface for a simpler use of the 'sbm' R package. It also contains useful functions to easily explore the 'sbm' package results. With this package you should be able to use the stochastic block model without any knowledge in R, get automatic reports and nice visuals, as well as learning the basic functions of 'sbm'.
Maintained by Theodore Vanrenterghem. Last updated 2 years ago.
3.70 score 6 scripts
sigbertklinke
HKRbook:Apps and Data for the Book "Introduction to Statistics"
Functions, Shiny apps and data for the book "Introduction to Statistics" by Wolfgang Karl Härdle, Sigbert Klinke, and Bernd Rönz (2015) <doi:10.1007/978-3-319-17704-5>.
Maintained by Sigbert Klinke. Last updated 2 years ago.
1 stars 3.70 scoresigbertklinke
smvgraph:Visualization and Clustering of Data in a Shiny App
Various visualisations of univariate and multivariate graphs (e.g. mosaic diagram, scatterplot matrix, Andrews curves, parallel coordinate diagram, radar diagram and Chernoff plots) as well as clustering methods (e.g. k-means, agglomerative, EM clustering and DBSCAN) are implemented as a Shiny app. The app allows interactive changes, e.g. of the order of variables. It is intended for use in teaching.
Maintained by Sigbert Klinke. Last updated 2 years ago.
3.70 score
miguel-sorrel
cdcatR:Cognitive Diagnostic Computerized Adaptive Testing
Provides a set of functions for conducting cognitive diagnostic computerized adaptive testing applications (Chen, 2009) <DOI:10.1007/s11336-009-9123-2>). It includes different item selection rules such us the global discrimination index (Kaplan, de la Torre, and Barrada (2015) <DOI:10.1177/0146621614554650>) and the nonparametric selection method (Chang, Chiu, and Tsai (2019) <DOI:10.1177/0146621618813113>), as well as several stopping rules. Functions for generating item banks and responses are also provided. To guide item bank calibration, model comparison at the item level can be conducted using the two-step likelihood ratio test statistic by Sorrel, de la Torre, Abad and Olea (2017) <DOI:10.1027/1614-2241/a000131>.
Maintained by Miguel A. Sorrel. Last updated 3 years ago.
5 stars 3.63 score 17 scripts
litgde
Spectran:Visual and Non-Visual Spectral Analysis of Light
Analyse light spectra for visual and non-visual (often called melanopic) needs, wrapped up in a Shiny App. 'Spectran' allows for the import of spectra in various CSV forms but also provides a wide range of example spectra and even the creation of own spectral power distributions. The goal of the app is to provide easy access and a visual overview of the spectral calculations underlying common parameters used in the field. It is thus ideal for educational purposes or the creation of presentation ready graphs in lighting research and application. 'Spectran' uses equations and action spectra described in CIE S026 (2018) <doi:10.25039/S026.2018>, DIN/TS 5031-100 (2021) <doi:10.31030/3287213>, and ISO/CIE 23539 (2023) <doi:10.25039/IS0.CIE.23539.2023>.
Maintained by Johannes Zauner. Last updated 6 months ago.
2 stars 3.60 score 3 scriptspaulgovan
WeibullR.shiny:A 'Shiny' App for Weibull Analysis
A 'Shiny' web application for life data analysis that depends on 'WeibullR' by David Silkworth and Jurgen Symynck (2022) <https://CRAN.R-project.org/package=WeibullR>, an R package for Weibull analysis.
Maintained by Paul Govan. Last updated 4 months ago.
life-data-analysisshinyweibull-analysis
3.54 score
kapsner
BiasCorrector:A GUI to Correct Measurement Bias in DNA Methylation Analyses
A GUI to correct measurement bias in DNA methylation analyses. The 'BiasCorrector' package just wraps the functions implemented in the 'R' package 'rBiasCorrection' into a shiny web application in order to make them more easily accessible. Publication: Kapsner et al. (2021) <doi:10.1002/ijc.33681>.
Maintained by Lorenz A. Kapsner. Last updated 6 months ago.
bias-correctiongene-methylationgeneticsguipcrshiny
2 stars 3.48 score 1 scripts
rgyoung6
DBTCShiny:Dada-BLAST-Taxon Assign-Condense Metabarcode Analysis 'shiny' Application
Metabarcoding analysis using the 'DBTC' package is implemented here using 'shiny' in an interactive graphical user interface to conduct Metabarcode analyses and visualize and filter results.
Maintained by Robert G Young. Last updated 10 months ago.
3.48 score 1 scripts
curycu
geodrawr:Making Geospatial Objects
Draw geospatial objects by clicks on the map. This packages can help data analyst who want to check their own geospatial hypothesis but has no ready-made geospatial objects.
Maintained by Heoncheol Ha. Last updated 4 years ago.
6 stars 3.48 score 6 scripts
lozalojo
memapp:The Moving Epidemic Method Web Application
The Moving Epidemic Method, created by T Vega and JE Lozano (2012, 2015) <doi:10.1111/j.1750-2659.2012.00422.x>, <doi:10.1111/irv.12330>, allows the weekly assessment of the epidemic and intensity status to help in routine respiratory infections surveillance in health systems. Allows the comparison of different epidemic indicators, timing and shape with past epidemics and across different regions or countries with different surveillance systems. Also, it gives a measure of the performance of the method in terms of sensitivity and specificity of the alert week. 'memapp' is a web application created in the Shiny framework for the 'mem' R package.
Maintained by Jose E. Lozano. Last updated 2 years ago.
3 stars 3.48 score 2 scripts
imamachi-n
bridger2:Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data
BRIC-seq is a genome-wide approach for determining RNA stability in mammalian cells. This package provides a series of functions for performing quality check of your BRIC-seq data, calculation of RNA half-life for each transcript and comparison of RNA half-lives between two conditions.
Maintained by Naoto Imamachi. Last updated 8 years ago.
bioinformaticsbric-seqhalf-lifengsrnarpkm-values
3 stars 3.43 score 18 scripts
laresbernardo
lareshiny:Lares 'shiny' Modules
Useful 'shiny' production-ready modules and helpers such as login window and visualization tools.
Maintained by Bernardo Lares. Last updated 2 years ago.
5 stars 3.40 score 2 scripts
yonghuidong
RawHummus:Raw Data Quality Control Tool for LC-MS System
Assess LC–MS system performance by visualizing instrument log files and monitoring raw quality control samples within a project.
Maintained by Yonghui Dong. Last updated 2 years ago.
lcmsmetabolomicsorbitrapquality-control
5 stars 3.40 score 2 scripts
myaseen208
StabilityApp:Stability Analysis App for GEI in Multi-Environment Trials
Provides tools for Genotype by Environment Interaction (GEI) analysis, using statistical models and visualizations to assess genotype performance across environments. It helps researchers explore interaction effects, stability, and adaptability in multi-environment trials, identifying the best-performing genotypes in different conditions. Which Win Where!
Maintained by Muhammad Yaseen. Last updated 5 months ago.
ammibiplotgeiggemetstability-analysis
3.30 score
bioc
levi:Landscape Expression Visualization Interface
The tool integrates data from biological networks with transcriptomes, displaying a heatmap with surface curves to evidence the altered regions.
Maintained by Jose Luiz Rybarczyk Filho. Last updated 5 months ago.
geneexpressionsequencingnetworksoftwarecpp
3.30 score 4 scripts
gwpcor
gwpcormapper:Geographically Weighted Partial Correlation Mapper
An interactive mapping tool for geographically weighted correlation and partial correlation. Geographically weighted partial correlation coefficients are calculated following (Percival and Tsutsumida, 2017)<doi:10.1553/giscience2017_01_s36> and are described in greater detail in (Tsutsumida et al., 2019)<doi:10.5194/ica-abs-1-372-2019> and (Percival et al., 2021)<arXiv:2101.03491>.
Maintained by Joseph Emile Honour Percival. Last updated 3 years ago.
3 stars 3.18 score 1 scripts
cran
iAdapt:Two-Stage Adaptive Dose-Finding Clinical Trial Design
Simulate and implement early phase two-stage adaptive dose-finding design for binary and quasi-continuous toxicity endpoints. See Chiuzan et al. (2018) for further reading <DOI:10.1080/19466315.2018.1462727>.
Maintained by Alyssa Vanderbeek. Last updated 4 years ago.
3.18 score
ku-awdc
EpiLinx:Interactive Visualization Tool for Nosocomial Outbreaks
What the package does (one paragraph).
Maintained by Anna Emilie Henius. Last updated 2 months ago.
3.18 score
farmse988
Poly4AT:Access 'INVEKOS' API for Field Polygons
A 'shiny' app that allows to access and use the 'INVEKOS' API for field polygons in Austria. API documentation is available at <https://gis.lfrz.gv.at/api/geodata/i009501/ogc/features/v1/>.
Maintained by Sebastian Wieser. Last updated 5 months ago.
3.18 score
lilyclements
carbonr:Calculate Carbon-Equivalent Emissions
Provides a flexible tool for calculating carbon-equivalent emissions. Mostly using data from the UK Government's Greenhouse Gas Conversion Factors report <https://www.gov.uk/government/publications/greenhouse-gas-reporting-conversion-factors-2023>, it facilitates transparent emissions calculations for various sectors, including travel, accommodation, and clinical activities. The package is designed for easy integration into R workflows, with additional support for 'shiny' applications and community-driven extensions.
Maintained by Lily Clements. Last updated 6 months ago.
3.16 score 29 scriptspromidat
discoveR:Exploratory Data Analysis System
Performs an exploratory data analysis through a 'shiny' interface. It includes basic methods such as the mean, median, mode, normality test, among others. It also includes clustering techniques such as Principal Components Analysis, Hierarchical Clustering and the K-Means Method.
Maintained by Oldemar Rodriguez. Last updated 2 years ago.
3 stars 3.03 score 18 scripts
learnitr
learnitgrid:Manage Rubrics or Assessment Grids for GitHub Repositories
Create and manage semi-automatically rubrics to assess GitHub projects (R scripts, R Markdown or Quarto files). Create directed projects where students have to complete documents and submit them to GitHub (classroom) so that they are evaluated using the rubric (or assessment grid).
Maintained by Philippe Grosjean. Last updated 10 months ago.
1 stars 3.00 score 7 scripts
amalan-constat
fitODBODRshiny:'Shiny' Application for R Package 'fitODBOD'
For binomial outcome data Alternate Binomial Distributions and Binomial Mixture Distributions are fitted when overdispersion is available.
Maintained by Amalan Mahendran. Last updated 6 months ago.
3.00 score
sergeitarasov
ontoFAST:Interactive Annotation of Characters with Biological Ontologies
Tools for annotating characters (character matrices) with anatomical and phenotype ontologies. Includes functions for visualising character annotations and creating simple queries using ontological relationships.
Maintained by Sergei Tarasov. Last updated 3 years ago.
annotationscharacter-matricescharactersontologyphylogenetics
2 stars 3.00 score 5 scriptsmyaseen208
PakPC:'shiny' App to Analyze Pakistan's Population Census Data
Provides tools for analyzing Pakistan's Population Censuses data via the 'PakPC2023' and 'PakPC2017' R packages. Designed for researchers, policymakers, and professionals, the app enables in-depth numerical and graphical analysis, including detailed cross-tabulations and insights. With diverse statistical models and visualization options, it supports informed decision-making in social and economic policy. This tool enhances users' ability to explore and interpret census data, providing valuable insights for effective planning and analysis across various fields.
Maintained by Muhammad Yaseen. Last updated 4 months ago.
1 stars 3.00 score 4 scripts
pilacuan-bonete-luis
LDABiplots:Biplot Graphical Interface for LDA Models
Contains the development of a tool that provides a web-based graphical user interface (GUI) to perform Biplots representations from a scraping of news from digital newspapers under the Bayesian approach of Latent Dirichlet Assignment (LDA) and machine learning algorithms. Contains LDA methods described by Blei , David M., Andrew Y. Ng and Michael I. Jordan (2003) <https://jmlr.org/papers/volume3/blei03a/blei03a.pdf>, and Biplot methods described by Gabriel K.R(1971) <doi:10.1093/biomet/58.3.453> and Galindo-Villardon P(1986) <https://diarium.usal.es/pgalindo/files/2012/07/Questiio.pdf>.
Maintained by Luis Pilacuan-Bonete. Last updated 3 years ago.
3.00 score 4 scripts
ijayc
shinyr:Data Insights Through Inbuilt R Shiny App
It builds dynamic R shiny based dashboards to analyze any CSV files. It provides simple dashboard design to subset the data, perform exploratory data analysis and preliminary machine learning (supervised and unsupervised). It also provides filters based on columns of interest.
Maintained by Jayachandra N. Last updated 2 months ago.
3.00 score
jinkim3
ezr:Easy Use of R via Shiny App for Basic Analyses of Experimental Data
Runs a Shiny App in the local machine for basic statistical and graphical analyses. The point-and-click interface of Shiny App enables obtaining the same analysis outputs (e.g., plots and tables) more quickly, as compared with typing the required code in R, especially for users without much experience or expertise with coding. Examples of possible analyses include tabulating descriptive statistics for a variable, creating histograms by experimental groups, and creating a scatter plot and calculating the correlation between two variables.
Maintained by Jin Kim. Last updated 4 years ago.
1 stars 3.00 score 2 scripts
learnitr
learnitdashboard:Shiny Dashboard for 'learnitr' Data
A dashboard to explore data generated by 'learnitr' code, such as the 'learnitdown', or the 'learnitgrid' R package. This is a lightweight learning analytics solution for the 'learnitr' ecosystem.
Maintained by Philippe Grosjean. Last updated 10 months ago.
learning-analyticsteaching-tools
2 stars 3.00 score 3 scriptsmyaseen208
PakNAcc:'shiny' App for National Accounts
Provides a comprehensive suite of tools for analyzing Pakistan's Quarterly National Accounts data. Users can gain detailed insights into Pakistan's economic performance, visualize quarterly trends, and detect patterns and anomalies in key economic indicators. Compare sector contributions—including agriculture, industry, and services—to understand their influence on economic growth or decline. Customize analyses by filtering and manipulating data to focus on specific areas of interest. Ideal for policymakers, researchers, and analysts aiming to make informed, data-driven decisions based on timely and detailed economic insights.
Maintained by Muhammad Yaseen. Last updated 5 months ago.
3.00 score
glotaran
paramGUI:A Shiny GUI for some Parameter Estimation Examples
Allows specification and fitting of some parameter estimation examples inspired by time-resolved spectroscopy via a Shiny GUI.
Maintained by Joris Snellenburg. Last updated 2 years ago.
educationestimationparameter-estimationshinyteaching
2 stars 3.00 score 6 scripts
markheckmann
OpenRepGrid.ic:Interpretive Clustering for Repertory Grids
Shiny UI to identify cliques of related constructs in repertory grid data. See Burr, King, & Heckmann (2020) <doi:10.1080/14780887.2020.1794088> for a description of the interpretive clustering (IC) method.
Maintained by Mark Heckmann. Last updated 1 years ago.
clusteringconstructsgridrepertoryrepgridshiny
2 stars 3.00 score 8 scripts
amalan-constat
SouthParkRshiny:Data and 'Shiny' Application for the Show 'SouthPark'
Ratings, votes, swear words and sentiments are analysed for the show 'SouthPark' through a 'Shiny' application after web scraping from 'IMDB' and the website <https://southpark.fandom.com/wiki/South_Park_Archives>.
Maintained by Amalan Mahendran. Last updated 1 years ago.
1 stars 2.70 score
tcoroller
monitOS:Monitoring Overall Survival in Pivotal Trials in Indolent Cancers
These guidelines are meant to provide a pragmatic, yet rigorous, help to drug developers and decision makers, since they are shaped by three fundamental ingredients: the clinically determined margin of detriment on OS that is unacceptably high (delta null); the benefit on OS that is plausible given the mechanism of action of the novel intervention (delta alt); and the quantity of information (i.e. survival events) it is feasible to accrue given the clinical and drug development setting. The proposed guidelines facilitate transparent discussions between stakeholders focusing on the risks of erroneous decisions and what might be an acceptable trade-off between power and the false positive error rate.
Maintained by Thibaud Coroller. Last updated 1 years ago.
2.70 score 4 scripts
atalay-k
drawsample:Draw Samples with the Desired Properties from a Data Set
A tool to sample data with the desired properties.Samples can be drawn by purposive sampling with determining distributional conditions, such as deviation from normality (skewness and kurtosis), and sample size in quantitative research studies. For purposive sampling, a researcher has something in mind and participants that fit the purpose of the study are included (Etikan,Musa, & Alkassim, 2015) <doi:10.11648/j.ajtas.20160501.11>.Purposive sampling can be useful for answering many research questions (Klar & Leeper, 2019) <doi:10.1002/9781119083771.ch21>.
Maintained by Kubra Atalay Kabasakal. Last updated 3 years ago.
1 stars 2.70 score 1 scripts
andrija-djurovic
monobinShiny:Shiny User Interface for 'monobin' Package
This is an add-on package to the 'monobin' package that simplifies its use. It provides shiny-based user interface (UI) that is especially handy for less experienced 'R' users as well as for those who intend to perform quick scanning of numeric risk factors when building credit rating models. The additional functions implemented in 'monobinShiny' that do no exist in 'monobin' package are: descriptive statistics, special case and outliers imputation. The function descriptive statistics is exported and can be used in 'R' sessions independently from the user interface, while special case and outlier imputation functions are written to be used with shiny UI.
Maintained by Andrija Djurovic. Last updated 3 years ago.
1 stars 2.70 score 6 scriptsijayc
netknitr:Knit Network Map for any Dataset
Designed to create interactive and visually compelling network maps using R Shiny. It allows users to quickly analyze CSV files and visualize complex relationships, structures, and connections within data by leveraging powerful network analysis libraries and dynamic web interfaces.
Maintained by Jayachandra N. Last updated 1 months ago.
2.70 scorecran
JustifyAlpha:Justifying Alpha Levels for Hypothesis Tests
Functions to justify alpha levels for statistical hypothesis tests by avoiding Lindley's paradox, or by minimizing or balancing error rates. For more information about the package please read the following: Maier & Lakens (2021) <doi:10.31234/osf.io/ts4r6>).
Maintained by Maximilian Maier. Last updated 4 years ago.
2.70 score
yaoxiangli
ShinyLink:'Shiny' Based Record Linkage Tool
A bridge is created between existing robust open-source record linkage algorithms and an urgently needed user-friendly platform that removes financial and technical barriers, setting a new standard for data interoperability in public health and bioinformatics. The 'fastLink' algorithms are used for matching. Ted Enamorado et al. (2019) <doi:10.1017/S0003055418000783>.
Maintained by Yaoxiang Li. Last updated 2 years ago.
2.70 score 6 scripts
wa-department-of-agriculture
WaCSE:Washington Climate Smart Estimator
The Washington Climate Smart Estimator (WaCSE) is a shiny application to explore greenhouse gas mitigation potential from different agricultural conservation practices across Washington's diverse counties.
Maintained by Jadey Ryan. Last updated 19 days ago.
8 stars 2.60 scorepromidat
predictoR:Predictive Data Analysis System
Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as K-Nearest Neighbors, Decision Trees, ADA Boosting, Extreme Gradient Boosting, Random Forest, Neural Networks, Deep Learning, Support Vector Machines and Bayesian Methods.
Maintained by Oldemar Rodriguez. Last updated 1 years ago.
1 stars 2.60 score 3 scripts
csoneson
ConfoundingExplorer:Confounding Explorer
This package provides a simple interactive application for investigating the effect of confounding between a signal of interest and a batch effect. It uses simulated data with user-specified effect sizes for both batch and condition effects. The user can also specify the number of samples in each condition and batch, and thereby the degree of confounding.
Maintained by Charlotte Soneson. Last updated 3 months ago.
regressionexperimentaldesignmultiplecomparisonbatcheffect
2 stars 2.60 score 3 scripts
homerhanumat
bcscr:Beginning Computer Science with R
Functions and datasets to accompany the text Beginning Computer Science with R (https://homerhanumat.github.io/r-notes).
Maintained by Homer White. Last updated 4 months ago.
2 stars 2.30 score 8 scripts
vharntzen
doublIn:Estimate Incubation or Latency Time using Doubly Interval Censored Observations
Visualize contact tracing data using a 'shiny' app and estimate the incubation or latency time of an infectious disease respecting the following characteristics in the analysis; (i) doubly interval censoring with (partly) overlapping or distinct windows; (ii) an infection risk corresponding to exponential growth; (iii) right truncation allowing for individual truncation times; (iv) different choices concerning the family of the distribution. For our earlier work, we refer to Arntzen et al. (2023) <doi:10.1002/sim.9726>. A paper describing our approach in detail will follow.
Maintained by Vera Arntzen. Last updated 10 months ago.
2.30 score 3 scripts
ethanbass
ShinyChromViewer:Shiny Gadget for Interactive Viewing and Exploration of Chromatograms
Shiny Gadget for interactive viewing and exploration of chromatograms.
Maintained by Ethan Bass. Last updated 2 years ago.
chromatographyhplchplc-dadhplc-uvopen-dataopen-scienceshinyshiny-apps
3 stars 2.18 scorecran
SRTsim:Simulator for Spatially Resolved Transcriptomics
An independent, reproducible, and flexible Spatially Resolved Transcriptomics (SRT) simulation framework that can be used to facilitate the development of SRT analytical methods for a wide variety of SRT-specific analyses. It utilizes spatial localization information to simulate SRT expression count data in a reproducible and scalable fashion. Two major simulation schemes are implemented in 'SRTsim': reference-based and reference-free.
Maintained by Jiaqiang Zhu. Last updated 7 months ago.
2.00 scoremedianasoft
MCPModPack:Simulation-Based Design and Analysis of Dose-Finding Trials
An efficient implementation of the MCPMod (Multiple Comparisons and Modeling) method to support a simulation-based design and analysis of dose-finding trials with normally distributed, binary and count endpoints (Bretz et al. (2005) <doi:10.1111/j.1541-0420.2005.00344.x>).
Maintained by Alex Dmitrienko. Last updated 2 years ago.
1 stars 2.00 score 1 scriptscran
tRigon:Toolbox for Integrative Pathomics Analysis
Processing and analysis of pathomics, omics and other medical datasets. 'tRigon' serves as a toolbox for descriptive and statistical analysis, correlations, plotting and many other methods for exploratory analysis of high-dimensional datasets.
Maintained by David Hoelscher. Last updated 7 months ago.
2.00 scorepromidat
forecasteR:Time Series Forecast System
A web application for displaying, analysing and forecasting univariate time series. Includes basic methods such as mean, naïve, seasonal naïve and drift, as well as more complex methods such as Holt-Winters Box,G and Jenkins, G (1976) <doi:10.1111/jtsa.12194> and ARIMA Brockwell, P.J. and R.A.Davis (1991) <doi:10.1007/978-1-4419-0320-4>.
Maintained by Oldemar Rodriguez. Last updated 2 years ago.
2.00 score 2 scripts
elakkkk
istat:Download and Manipulate Data from Istat
Download data from Istat (Italian Institute of Statistics) database, both old and new provider (respectively, <http://dati.istat.it/> and <https://esploradati.istat.it/databrowser/>). Additional functions for manipulating data are provided. Moreover, a 'shiny' application called 'shinyIstat' can be used to search, download and filter datasets in an easier way.
Maintained by Elena Gradi. Last updated 7 months ago.
2.00 score 2 scripts
byadu
modgetxl:A 'shiny' Module for Reading Excel Sheets
This is a shiny module that presents a file picker user interface to get an Excel file name, and reads the Excel sheets using 'readxl' package and returns the resulting sheet(s) as a vector and data in dataframe(s).
Maintained by Yadu Balehosur. Last updated 5 years ago.
2.00 score 4 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 4 months ago.
2.00 score 1 scripts
ccicb
CRUX:Easily explore patterns of somatic variation in cancer using 'CRUX'
Shiny app for exploring somatic variation in cancer. Powered by maftools.
Maintained by Sam El-Kamand. Last updated 1 years ago.
2 stars 2.00 score 5 scripts
pogibas
bdDwC:Darwinizer: Darwin Core (DwC) Field Names Standardization
The 'shiny' application 'bdDwC' makes biodiversity data field names Darwin Core compatible.
Maintained by Povilas Gibas. Last updated 7 years ago.
1.81 score 13 scriptscran
ShinyQuickStarter:'RStudio' Addin for Building Shiny Apps per Drag & Drop
This 'RStudio' addin makes the creation of 'Shiny' and 'ShinyDashboard' apps more efficient. Besides the necessary folder structure, entire apps can be created using a drag and drop interface and customized with respect to a specific use case. The addin allows the export of the required user interface and server code at any time. By allowing the creation of modules, the addin can be used throughout the entire app development process.
Maintained by Leon Binder. Last updated 4 years ago.
6 stars 1.78 score
zhanxw
cromwellDashboard:A Dashboard to Visualize Scientific Workflows in 'Cromwell'
A dashboard supports the usage of 'cromwell'. 'Cromwell' is a scientific workflow engine for command line users. This package utilizes 'cromwell' REST APIs and provides these convenient functions: timing diagrams for running workflows, 'cromwell' engine status, a tabular workflow list. For more information about 'cromwell', visit <http://cromwell.readthedocs.io>.
Maintained by Xiaowei Zhan. Last updated 7 years ago.
1.70 score 4 scripts
sowmyachandrasekaran17
EventDetectGUI:Graphical User Interface for the 'EventDetectR' Package
A graphical user interface for open source event detection.
Maintained by Sowmya Chandrasekaran. Last updated 5 years ago.
1.70 score 2 scriptscran
regressoR:Regression Data Analysis System
Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as linear regression, penalized regression, k-nearest neighbors, decision trees, ada boosting, extreme gradient boosting, random forest, neural networks, deep learning and support vector machines.
Maintained by Oldemar Rodriguez. Last updated 5 months ago.
2 stars 1.30 score
wenchao-ma
ACTCD:Asymptotic Classification Theory for Cognitive Diagnosis
Cluster analysis for cognitive diagnosis based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; <doi:10.1007/s11336-009-9125-0>). Given the sample statistic of sum-scores, cluster analysis techniques can be used to classify examinees into latent classes based on their attribute patterns. In addition to the algorithms used to classify data, three labeling approaches are proposed to label clusters so that examinees' attribute profiles can be obtained.
Maintained by Wenchao Ma. Last updated 1 years ago.
1.00 score 7 scripts
huseyinyildiz35
DIFshiny:Differential Item Functioning via Shiny Application
Differential Item Functioning (DIF) Analysis with shiny application interfaces. You can run the functions in this package without any arguments and perform your DIF analysis using user-friendly interfaces.
Maintained by Huseyin Yildiz. Last updated 4 years ago.
1.00 score
iankopacka
eufmdis.adapt:Analyse 'EuFMDiS' Output Files via a Shiny App
Analyses 'EuFMDiS' output files in a Shiny App. The distributions of relevant output parameters are described in form of tables (quantiles) and plots. The App is called using eufmdis.adapt::run_adapt().
Maintained by Ian Kopacka. Last updated 2 years ago.
1.00 score
wilsonrp
T2Qv:Control Qualitative Variables
Covers k-table control analysis using multivariate control charts for qualitative variables using fundamentals of multiple correspondence analysis and multiple factor analysis. The graphs can be shown in a flat or interactive way, in the same way all the outputs can be shown in an interactive shiny panel.
Maintained by Wilson Rojas-Preciado. Last updated 1 years ago.
1.00 score
eguidotti
yuimaGUI:A Graphical User Interface for the 'yuima' Package
Provides a graphical user interface for the 'yuima' package.
Maintained by Emanuele Guidotti. Last updated 3 years ago.
1.00 score 2 scripts