Showing 80 of total 80 results (show query)
talgalili
heatmaply:Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2'
Create interactive cluster 'heatmaps' that can be saved as a stand- alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' to 'heatmap.2' with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'.
Maintained by Tal Galili. Last updated 9 months ago.
d3-heatmapdendextenddendrogramggplot2heatmapplotly
386 stars 14.21 score 2.0k scripts 45 dependents
mhahsler
seriation:Infrastructure for Ordering Objects Using Seriation
Infrastructure for ordering objects with an implementation of several seriation/sequencing/ordination techniques to reorder matrices, dissimilarity matrices, and dendrograms. Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.
Maintained by Michael Hahsler. Last updated 5 days ago.
combinatorial-optimizationordinationseriationfortran
77 stars 14.11 score 640 scripts 79 dependents
tidymodels
corrr:Correlations in R
A tool for exploring correlations. It makes it possible to easily perform routine tasks when exploring correlation matrices such as ignoring the diagonal, focusing on the correlations of certain variables against others, or rearranging and visualizing the matrix in terms of the strength of the correlations.
Maintained by Max Kuhn. Last updated 1 years ago.
593 stars 13.82 score 2.9k scripts 7 dependents
pecanproject
PEcAn.data.atmosphere:PEcAn Functions Used for Managing Climate Driver Data
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The PECAn.data.atmosphere package converts climate driver data into a standard format for models integrated into PEcAn. As a standalone package, it provides an interface to access diverse climate data sets.
Maintained by David LeBauer. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
216 stars 11.63 score 64 scripts 14 dependentsmhahsler
arulesViz:Visualizing Association Rules and Frequent Itemsets
Extends package 'arules' with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration. Michael Hahsler (2017) <doi:10.32614/RJ-2017-047>.
Maintained by Michael Hahsler. Last updated 7 months ago.
arulesassociation-rulesfrequent-itemsetsinteractive-visualizationsvisualization
54 stars 11.03 score 1.7k scripts 2 dependentspecanproject
PEcAn.assim.batch:PEcAn Functions Used for Ecological Forecasts and Reanalysis
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.
Maintained by Istem Fer. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
216 stars 9.97 score 20 scripts 2 dependentspecanproject
PEcAnRTM:PEcAn Functions Used for Radiative Transfer Modeling
Functions for performing forward runs and inversions of radiative transfer models (RTMs). Inversions can be performed using maximum likelihood, or more complex hierarchical Bayesian methods. Underlying numerical analyses are optimized for speed using Fortran code.
Maintained by Alexey Shiklomanov. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsfortranjagscpp
216 stars 9.72 score 132 scripts
bioc
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
OUTRIDER:OUTRIDER - OUTlier in RNA-Seq fInDER
Identification of aberrant gene expression in RNA-seq data. Read count expectations are modeled by an autoencoder to control for confounders in the data. Given these expectations, the RNA-seq read counts are assumed to follow a negative binomial distribution with a gene-specific dispersion. Outliers are then identified as read counts that significantly deviate from this distribution. Furthermore, OUTRIDER provides useful plotting functions to analyze and visualize the results.
Maintained by Christian Mertes. Last updated 5 months ago.
immunooncologyrnaseqtranscriptomicsalignmentsequencinggeneexpressiongeneticscount-datadiagnosticsexpression-analysismendelian-geneticsoutlier-detectionrna-seqopenblascpp
50 stars 9.07 score 110 scripts 1 dependentspecanproject
PEcAn.all:PEcAn Functions Used for Ecological Forecasts and Reanalysis
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.
Maintained by David LeBauer. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
216 stars 9.02 score 266 scriptspecanproject
PEcAn.MAAT:PEcAn Package for Integration of the MAAT Model
This module provides functions to wrap the MAAT model into the PEcAn workflows.
Maintained by Shawn Serbin. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
216 stars 8.97 score 12 scriptspecanproject
PEcAn.BIOCRO:PEcAn Package for Integration of the BioCro Model
This module provides functions to link BioCro to PEcAn.
Maintained by David LeBauer. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
216 stars 8.96 score 23 scriptspecanproject
PEcAn.workflow:PEcAn Functions Used for Ecological Forecasts and Reanalysis
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. This package provides workhorse functions that can be used to run the major steps of a PEcAn analysis.
Maintained by David LeBauer. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
216 stars 8.85 score 15 scripts 4 dependentspecanproject
PEcAn.ED2:PEcAn Package for Integration of ED2 Model
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. This package provides functions to link the Ecosystem Demography Model, version 2, to PEcAn.
Maintained by Mike Dietze. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
216 stars 8.76 score 145 scriptsbioc
FRASER:Find RAre Splicing Events in RNA-Seq Data
Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.
Maintained by Christian Mertes. Last updated 5 months ago.
rnaseqalternativesplicingsequencingsoftwaregeneticscoverageaberrant-splicingdiagnosticsoutlier-detectionrare-diseaserna-seqsplicingopenblascpp
44 stars 8.53 score 155 scriptspecanproject
PEcAn.SIPNET:PEcAn Functions Used for Ecological Forecasts and Reanalysis
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.
Maintained by Mike Dietze. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
216 stars 8.38 score 61 scripts
chuhousen
amerifluxr:Interface to 'AmeriFlux' Data Services
Programmatic interface to the 'AmeriFlux' database (<https://ameriflux.lbl.gov/>). Provide query, download, and data summary tools.
Maintained by Housen Chu. Last updated 3 months ago.
amerifluxapicarbon-fluxdatatime-series
22 stars 8.36 score 29 scripts 15 dependentspecanproject
PEcAnAssimSequential:PEcAn Functions Used for Ecological Forecasts and Reanalysis
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.
Maintained by Mike Dietze. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
216 stars 8.14 score 35 scriptsbioc
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 scriptspecanproject
PEcAn.MAESPA:PEcAn Functions Used for Ecological Forecasts and Reanalysis using MAESPA
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.This package allows for MAESPA to be run through the PEcAN workflow.
Maintained by Tony Gardella. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
216 stars 7.59 score 2 scriptspecanproject
PEcAn.PRELES:PEcAn Package for Integration of the PRELES Model
This module provides functions to run the PREdict Light use efficiency Evapotranspiration and Soil moisture (PRELES) model on the PEcAn project. The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool designed to simplify the management of model parameterization,execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.
Maintained by Tony Gardella. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
216 stars 7.59 score 4 scriptspecanproject
PEcAn.BASGRA:PEcAn Package for Integration of the BASGRA Model
This module provides functions to link the BASGRA model to PEcAn.
Maintained by Istem Fer. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsfortranglibc
216 stars 7.59 score 1 scriptspecanproject
PEcAn.JULES:PEcAn Package for Integration of the JULES Model
This module provides functions to link the (JULES) to PEcAn.
Maintained by Mike Dietze. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
216 stars 7.59 scorepecanproject
PEcAn.LDNDC:PEcAn package for integration of the LDNDC model
This module provides functions to link the (LDNDC) to PEcAn.
Maintained by Henri Kajasilta. Last updated 8 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
216 stars 7.59 score
alaninglis
vivid:Variable Importance and Variable Interaction Displays
A suite of plots for displaying variable importance and two-way variable interaction jointly. Can also display partial dependence plots laid out in a pairs plot or 'zenplots' style.
Maintained by Alan Inglis. Last updated 8 months ago.
21 stars 7.39 score 39 scriptsbioc
sechm:sechm: Complex Heatmaps from a SummarizedExperiment
sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package.
Maintained by Pierre-Luc Germain. Last updated 1 months ago.
6 stars 7.03 score 60 scripts 2 dependentsbioc
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
mingzehuang
latentcor:Fast Computation of Latent Correlations for Mixed Data
The first stand-alone R package for computation of latent correlation that takes into account all variable types (continuous/binary/ordinal/zero-inflated), comes with an optimized memory footprint, and is computationally efficient, essentially making latent correlation estimation almost as fast as rank-based correlation estimation. The estimation is based on latent copula Gaussian models. For continuous/binary types, see Fan, J., Liu, H., Ning, Y., and Zou, H. (2017). For ternary type, see Quan X., Booth J.G. and Wells M.T. (2018) <arXiv:1809.06255>. For truncated type or zero-inflated type, see Yoon G., Carroll R.J. and Gaynanova I. (2020) <doi:10.1093/biomet/asaa007>. For approximation method of computation, see Yoon G., Müller C.L. and Gaynanova I. (2021) <doi:10.1080/10618600.2021.1882468>. The latter method uses multi-linear interpolation originally implemented in the R package <https://cran.r-project.org/package=chebpol>.
Maintained by Mingze Huang. Last updated 3 years ago.
data-analysisdata-miningdata-processingdata-sciencedata-structuresmachine-learningmixed-typesstatistics
16 stars 6.65 score 46 scripts 1 dependentsbioc
ViSEAGO:ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontology (GO) analysis of complex experimental design with multiple comparisons of interest. It allows to study large-scale datasets together and visualize GO profiles to capture biological knowledge. The acronym stands for three major concepts of the analysis: Visualization, Semantic similarity and Enrichment Analysis of Gene Ontology. It provides access to the last current GO annotations, which are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot databases for several species. Using available R packages and novel developments, ViSEAGO extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity. ViSEAGO has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility.
Maintained by Aurelien Brionne. Last updated 3 months ago.
softwareannotationgogenesetenrichmentmultiplecomparisonclusteringvisualization
6.64 score 22 scripts
bioc
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 19 days ago.
softwaretranscriptomicsrnaseqalternativesplicingcoveragedifferentialsplicingdifferentialexpressionguisequencingcppopenmp
16 stars 6.41 score 8 scripts
rickhelmus
patRoon:Workflows for Mass-Spectrometry Based Non-Target Analysis
Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.
Maintained by Rick Helmus. Last updated 10 days ago.
mass-spectrometrynon-targetcppopenjdk
65 stars 6.24 score 43 scripts
lhdjung
scrutiny:Error Detection in Science
Test published summary statistics for consistency (Brown and Heathers, 2017, <doi:10.1177/1948550616673876>; Allard, 2018, <https://aurelienallard.netlify.app/post/anaytic-grimmer-possibility-standard-deviations/>; Heathers and Brown, 2019, <https://osf.io/5vb3u/>). The package also provides infrastructure for implementing new error detection techniques.
Maintained by Lukas Jung. Last updated 6 months ago.
8 stars 6.22 score 38 scripts
david-barnett
microViz:Microbiome Data Analysis and Visualization
Microbiome data visualization and statistics tools built upon phyloseq.
Maintained by David Barnett. Last updated 4 months ago.
microbiomemicrobiome-analysismicrobiota
114 stars 6.22 score 480 scriptsbioc
metaseqR2:An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.
Maintained by Panagiotis Moulos. Last updated 19 days ago.
softwaregeneexpressiondifferentialexpressionworkflowsteppreprocessingqualitycontrolnormalizationreportwritingrnaseqtranscriptionsequencingtranscriptomicsbayesianclusteringcellbiologybiomedicalinformaticsfunctionalgenomicssystemsbiologyimmunooncologyalternativesplicingdifferentialsplicingmultiplecomparisontimecoursedataimportatacseqepigeneticsregressionproprietaryplatformsgenesetenrichmentbatcheffectchipseq
7 stars 6.05 score 3 scriptsbioc
dar:Differential Abundance Analysis by Consensus
Differential abundance testing in microbiome data challenges both parametric and non-parametric statistical methods, due to its sparsity, high variability and compositional nature. Microbiome-specific statistical methods often assume classical distribution models or take into account compositional specifics. These produce results that range within the specificity vs sensitivity space in such a way that type I and type II error that are difficult to ascertain in real microbiome data when a single method is used. Recently, a consensus approach based on multiple differential abundance (DA) methods was recently suggested in order to increase robustness. With dar, you can use dplyr-like pipeable sequences of DA methods and then apply different consensus strategies. In this way we can obtain more reliable results in a fast, consistent and reproducible way.
Maintained by Francesc Catala-Moll. Last updated 16 days ago.
softwaresequencingmicrobiomemetagenomicsmultiplecomparisonnormalizationbioconductorbiomarker-discoverydifferential-abundance-analysisfeature-selectionmicrobiologyphyloseq
2 stars 5.98 score 8 scripts
yonicd
shinyHeatmaply:Deploy 'heatmaply' using 'shiny'
Access functionality of the 'heatmaply' package through 'Shiny UI'.
Maintained by Jonathan Sidi. Last updated 5 years ago.
47 stars 5.95 score 42 scripts 1 dependentsbioc
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 scripts
cbhurley
condvis2:Interactive Conditional Visualization for Supervised and Unsupervised Models in Shiny
Constructs a shiny app function with interactive displays for conditional visualization of models, data and density functions. An extended version of package 'condvis'. Catherine B. Hurley, Mark O'Connell,Katarina Domijan (2021) <10.1080/10618600.2021.1983439>.
Maintained by Catherine Hurley. Last updated 3 years ago.
6 stars 5.86 score 16 scripts 1 dependents
bayer-group
adepro:A 'shiny' Application for the (Audio-)Visualization of Adverse Event Profiles
Contains a 'shiny' application called AdEPro (Animation of Adverse Event Profiles) which (audio-)visualizes adverse events occurring in clinical trials. As this data is usually considered sensitive, this tool is provided as a stand-alone application that can be launched from any local machine on which the data is stored.
Maintained by Nicole Rethemeier. Last updated 7 days ago.
adverse-eventsbayer-not-classifiedbayer-reg-nonebeat-not-applicableclinical-trialsdata-insightsshiny-appsvisualization
7 stars 5.84 score 11 scripts
trangdata
treeheatr:Heatmap-Integrated Decision Tree Visualizations
Creates interpretable decision tree visualizations with the data represented as a heatmap at the tree's leaf nodes. 'treeheatr' utilizes the customizable 'ggparty' package for drawing decision trees.
Maintained by Trang Le. Last updated 2 years ago.
datavizdecision-treesggplotheatmapvisualization
57 stars 5.71 score 18 scriptsbioc
SEtools:SEtools: tools for working with SummarizedExperiment
This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details).
Maintained by Pierre-Luc Germain. Last updated 5 months ago.
2 stars 5.64 score 72 scriptscbhurley
bullseye:Visualising Multiple Pairwise Variable Correlations and Other Scores
We provide a tidy data structure and visualisations for multiple or grouped variable correlations, general association measures scagnostics and other pairwise scores suitable for numerical, ordinal and nominal variables. Supported measures include distance correlation, maximal information, ace correlation, Kendall's tau, and polychoric correlation.
Maintained by Catherine Hurley. Last updated 24 days ago.
2 stars 5.58 score 14 scripts
keefe-murphy
MEDseq:Mixtures of Exponential-Distance Models with Covariates
Implements a model-based clustering method for categorical life-course sequences relying on mixtures of exponential-distance models introduced by Murphy et al. (2021) <doi:10.1111/rssa.12712>. A range of flexible precision parameter settings corresponding to weighted generalisations of the Hamming distance metric are considered, along with the potential inclusion of a noise component. Gating covariates can be supplied in order to relate sequences to baseline characteristics and sampling weights are also accommodated. The models are fitted using the EM algorithm and tools for visualising the results are also provided.
Maintained by Keefe Murphy. Last updated 21 days ago.
distance-based-clusteringmixture-of-expertsmodel-based-clusteringsequence-analysis
5 stars 5.49 score 25 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 scriptsbioc
MotifPeeker:Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo discovered motifs enriched in the datasets and compared with known motifs.
Maintained by Hiranyamaya Dash. Last updated 3 months ago.
epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsmotifdiscoverysequencematchingsoftwarealignmentbioconductorbioconductor-packagechip-seqepigenomicsinteractive-reportmotif-enrichment-analysis
2 stars 5.48 score 6 scriptsbioc
GEOexplorer:GEOexplorer: a webserver for gene expression analysis and visualisation
GEOexplorer is a webserver and R/Bioconductor package and web application that enables users to perform gene expression analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).
Maintained by Guy Hunt. Last updated 5 months ago.
softwaregeneexpressionmrnamicroarraydifferentialexpressionmicroarraymicrornaarraytranscriptomicsrnaseq
5 stars 5.32 score 14 scripts
signaturescience
skater:Utilities for SNP-Based Kinship Analysis
Utilities for single nucleotide polymorphism (SNP) based kinship analysis testing and evaluation. The 'skater' package contains functions for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing identity by descent (IBD) segment data. Package functions and methods are described in Turner et al. (2021) "skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation" <doi:10.1101/2021.07.21.453083>.
Maintained by Stephen Turner. Last updated 2 years ago.
9 stars 5.26 score 7 scriptsbioc
DegNorm:DegNorm: degradation normalization for RNA-seq data
This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy.
Maintained by Ji-Ping Wang. Last updated 5 months ago.
rnaseqnormalizationgeneexpressionalignmentcoveragedifferentialexpressionbatcheffectsoftwaresequencingimmunooncologyqualitycontroldataimportopenblascppopenmp
1 stars 5.08 score 3 scriptsbioc
shinyepico:ShinyÉPICo
ShinyÉPICo is a graphical pipeline to analyze Illumina DNA methylation arrays (450k or EPIC). It allows to calculate differentially methylated positions and differentially methylated regions in a user-friendly interface. Moreover, it includes several options to export the results and obtain files to perform downstream analysis.
Maintained by Octavio Morante-Palacios. Last updated 5 months ago.
differentialmethylationdnamethylationmicroarraypreprocessingqualitycontrol
5 stars 5.00 score 1 scriptsbioc
broadSeq:broadSeq : for streamlined exploration of RNA-seq data
This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.
Maintained by Rishi Das Roy. Last updated 5 months ago.
geneexpressiondifferentialexpressionrnaseqtranscriptomicssequencingcoveragegenesetenrichmentgo
4 stars 5.00 score 7 scriptsbioc
mspms:Tools for the analysis of MSP-MS data
This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.
Maintained by Charlie Bayne. Last updated 4 months ago.
proteomicsmassspectrometrypreprocessingproteaseproteomics-data-analysis
4.95 score 4 scriptsbioc
methylscaper:Visualization of Methylation Data
methylscaper is an R package for processing and visualizing data jointly profiling methylation and chromatin accessibility (MAPit, NOMe-seq, scNMT-seq, nanoNOMe, etc.). The package supports both single-cell and single-molecule data, and a common interface for jointly visualizing both data types through the generation of ordered representational methylation-state matrices. The Shiny app allows for an interactive seriation process of refinement and re-weighting that optimally orders the cells or DNA molecules to discover methylation patterns and nucleosome positioning.
Maintained by Bacher Rhonda. Last updated 5 months ago.
dnamethylationepigeneticssequencingvisualizationsinglecellnucleosomepositioning
1 stars 4.90 score 3 scriptsbioc
PolySTest:PolySTest: Detection of differentially regulated features. Combined statistical testing for data with few replicates and missing values
The complexity of high-throughput quantitative omics experiments often leads to low replicates numbers and many missing values. We implemented a new test to simultaneously consider missing values and quantitative changes, which we combined with well-performing statistical tests for high confidence detection of differentially regulated features. The package contains functions to run the test and to visualize the results.
Maintained by Veit Schwämmle. Last updated 4 months ago.
massspectrometryproteomicssoftwaredifferentialexpression
4.86 score 12 scripts
irinagain
mixedCCA:Sparse Canonical Correlation Analysis for High-Dimensional Mixed Data
Semi-parametric approach for sparse canonical correlation analysis which can handle mixed data types: continuous, binary and truncated continuous. Bridge functions are provided to connect Kendall's tau to latent correlation under the Gaussian copula model. The methods are described in Yoon, Carroll and Gaynanova (2020) <doi:10.1093/biomet/asaa007> and Yoon, Mueller and Gaynanova (2021) <doi:10.1080/10618600.2021.1882468>.
Maintained by Irina Gaynanova. Last updated 3 years ago.
21 stars 4.75 score 27 scripts
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 6 months ago.
7 stars 4.62 score
fcampelo
CALANGO:Comparative Analysis with Annotation-Based Genomic Components
A first-principle, phylogeny-aware comparative genomics tool for investigating associations between terms used to annotate genomic components (e.g., Pfam IDs, Gene Ontology terms,) with quantitative or rank variables such as number of cell types, genome size, or density of specific genomic elements. See the project website for more information, documentation and examples, and <doi:10.1016/j.patter.2023.100728> for the full paper.
Maintained by Felipe Campelo. Last updated 7 months ago.
2 stars 4.60 score 4 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
qmtools:Quantitative Metabolomics Data Processing Tools
The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. This package also offers a convenient way to compute empirical Bayes statistics for which metabolic features are different between two sets of study samples. Several functions in this package could also be used in other types of omics data.
Maintained by Jaehyun Joo. Last updated 5 months ago.
metabolomicspreprocessingnormalizationdimensionreductionmassspectrometry
1 stars 4.30 score 5 scriptsbioc
HarmonizR:Handles missing values and makes more data available
An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.
Maintained by Simon Schlumbohm. Last updated 5 months ago.
4.20 score 16 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
cysouw
qlcVisualize:Visualization for Quantitative Language Comparison
Collection of visualizations as used in quantitative language comparison. Currently implemented are visualisations dealing nominal data with multiple levels ("level map" and "factor map"), and assistance for making weighted geographical Voronoi-maps ("weighted map").
Maintained by Michael Cysouw. Last updated 6 months ago.
4.03 score 24 scriptsbioc
scTensor:Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor.
Maintained by Koki Tsuyuzaki. Last updated 5 months ago.
dimensionreductionsinglecellsoftwaregeneexpression
4.00 score 2 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 scripts
william-swl
baizer:Useful Functions for Data Processing
In ancient Chinese mythology, Bai Ze is a divine creature that knows the needs of everything. 'baizer' provides data processing functions frequently used by the author. Hope this package also knows what you want!
Maintained by William Song. Last updated 1 years ago.
dataframenumbersstringstidyverse
6 stars 3.95 score 5 scripts 1 dependentscbhurley
DendSer:Dendrogram Seriation: Ordering for Visualisation
Re-arranges a dendrogram to optimize visualisation-based cost functions.
Maintained by Catherine Hurley. Last updated 3 years ago.
3.74 score 27 scripts 5 dependentsalaninglis
corrViz:Visualise Correlations
An investigative tool designed to help users visualize correlations between variables in their datasets. This package aims to provide an easy and effective way to explore and visualize these correlations, making it easier to interpret and communicate results.
Maintained by Alan Inglis. Last updated 1 years ago.
1 stars 3.70 score 4 scriptswilliam-swl
plutor:Useful Functions for Visualization
In ancient Roman mythology, 'Pluto' was the ruler of the underworld and presides over the afterlife. 'Pluto' was frequently conflated with 'Plutus', the god of wealth, because mineral wealth was found underground. When plotting with R, you try once, twice, practice again and again, and finally you get a pretty figure you want. It's a 'plot tour', a tour about repetition and reward. Hope 'plutor' helps you on the tour!
Maintained by William Song. Last updated 1 years ago.
3 stars 3.62 score 28 scripts
david-hammond
tidymodlr:An R6 Class to Perform Analysis on Long Tidy Data
Transforms long data into a matrix form to allow for ease of input into modelling packages for regression, principal components, imputation or machine learning. It does this by pivoting on user defined columns, generating a key-value table for variable names to ensure one-to-one mappings are preserved. It is particularly useful when the indicator names in the columns are long descriptive strings, for example "Energy imports, net (% of energy use)". High level analysis wrapper functions for correlation and principal components analysis are provided.
Maintained by David Hammond. Last updated 7 months ago.
3.48 score 4 scripts
philboileau
neatmaps:Heatmaps for Multiple Network Data
Simplify the exploratory data analysis process for multiple network data sets with the help of hierarchical clustering, consensus clustering and heatmaps. Multiple network data consists of multiple disjoint networks that have common variables (e.g. ego networks). This package contains the necessary tools for exploring such data, from the data pre-processing stage to the creation of dynamic visualizations.
Maintained by Philippe Boileau. Last updated 3 years ago.
1 stars 2.70 score 7 scripts
joe-chelladurai
starry:Explore Data with Plots and Tables
Provides modular functions and applications for quickly generating plots and tables. Each modular function opens a graphical user interface providing the user with options to create and customise plots and tables.
Maintained by Joe Chelladurai. Last updated 2 years ago.
1 stars 2.70 score 1 scripts
wjschne
WJSmisc:Miscellaneous functions from W. Joel Schneider
Several functions I find useful.
Maintained by W. Joel Schneider. Last updated 2 years ago.
5 stars 2.40 score 10 scripts
cran
ClusteredMutations:Location and Visualization of Clustered Somatic Mutations
Identification and visualization of groups of closely spaced mutations in the DNA sequence of cancer genome. The extremely mutated zones are searched in the symmetric dissimilarity matrix using the anti-Robinson matrix properties. Different data sets are obtained to describe and plot the clustered mutations information.
Maintained by David Lora. Last updated 9 years ago.
2.00 scorecran
popstudy:Applied Techniques to Demographic and Time Series Analysis
The use of overparameterization is proposed with combinatorial analysis to test a broader spectrum of possible ARIMA models. In the selection of ARIMA models, the most traditional methods such as correlograms or others, do not usually cover many alternatives to define the number of coefficients to be estimated in the model, which represents an estimation method that is not the best. The popstudy package contains several tools for statistical analysis in demography and time series based in Shryock research (Shryock et. al. (1980) <https://books.google.co.cr/books?id=8Oo6AQAAMAAJ>).
Maintained by Cesar Gamboa-Sanabria. Last updated 1 years ago.
1.70 score
blansche
fdm2id:Data Mining and R Programming for Beginners
Contains functions to simplify the use of data mining methods (classification, regression, clustering, etc.), for students and beginners in R programming. Various R packages are used and wrappers are built around the main functions, to standardize the use of data mining methods (input/output): it brings a certain loss of flexibility, but also a gain of simplicity. The package name came from the French "Fouille de Données en Master 2 Informatique Décisionnelle".
Maintained by Alexandre Blansché. Last updated 2 years ago.
1 stars 1.62 score 42 scriptscran
RMaCzek:Czekanowski's Diagrams
Allows for production of Czekanowski's Diagrams with clusters. See K. Bartoszek, A. Vasterlund (2020) <doi:10.2478/bile-2020-0008> and K. Bartoszek, Y. Luo (2023) <doi:10.14708/ma.v51i2.7259>.
Maintained by Krzysztof Bartoszek. Last updated 9 months ago.
1.00 scorecran
TELP:Social Representation Theory Application: The Free Evocation of Words Technique
Using The Free Evocation of Words Technique method with some functions, this package will make a social representation and other analysis. The Free Evocation of Words Technique consists of collecting a number of words evoked by a subject facing exposure to an inducer term. The purpose of this technique is to understand the relationships created between words evoked by the individual and the inducer term. This technique is included in the theory of social representations, therefore, on the information transmitted by an individual, seeks to create a profile that define a social group.
Maintained by Gabriel Henrique Oliveira Assuncao. Last updated 2 years ago.
1.00 score