Showing 200 of total 619 results (show query)
thomasp85
patchwork:The Composer of Plots
The 'ggplot2' package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. 'patchwork' is a package that expands the API to allow for arbitrarily complex composition of plots by, among others, providing mathematical operators for combining multiple plots. Other packages that try to address this need (but with a different approach) are 'gridExtra' and 'cowplot'.
Maintained by Thomas Lin Pedersen. Last updated 4 days ago.
ggplot-extensionggplot2visualization
2.5k stars 19.83 score 82k scripts 657 dependents
slowkow
ggrepel:Automatically Position Non-Overlapping Text Labels with 'ggplot2'
Provides text and label geoms for 'ggplot2' that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.
Maintained by Kamil Slowikowski. Last updated 5 months ago.
1.2k stars 19.20 score 37k scripts 1.2k dependents
nanxstats
ggsci:Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
A collection of 'ggplot2' color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.
Maintained by Nan Xiao. Last updated 9 months ago.
color-palettesdata-visualizationggplot2ggscisci-fiscientific-journalsvisualization
680 stars 18.00 score 26k scripts 438 dependents
taiyun
corrplot:Visualization of a Correlation Matrix
Provides a visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.
Maintained by Taiyun Wei. Last updated 6 months ago.
323 stars 17.66 score 28k scripts 517 dependents
bioc
clusterProfiler:A universal enrichment tool for interpreting omics data
This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.
Maintained by Guangchuang Yu. Last updated 4 months ago.
annotationclusteringgenesetenrichmentgokeggmultiplecomparisonpathwaysreactomevisualizationenrichment-analysisgsea
1.1k stars 17.03 score 11k scripts 48 dependentsthomasp85
ggraph:An Implementation of Grammar of Graphics for Graphs and Networks
The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.
Maintained by Thomas Lin Pedersen. Last updated 1 years ago.
ggplot-extensionggplot2graph-visualizationnetwork-visualizationvisualizationcpp
1.1k stars 16.96 score 9.2k scripts 111 dependentsbioc
ComplexHeatmap:Make Complex Heatmaps
Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.
Maintained by Zuguang Gu. Last updated 5 months ago.
softwarevisualizationsequencingclusteringcomplex-heatmapsheatmap
1.3k stars 16.93 score 16k scripts 151 dependentsbioc
ggtree:an R package for visualization of tree and annotation data
'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.
Maintained by Guangchuang Yu. Last updated 5 months ago.
alignmentannotationclusteringdataimportmultiplesequencealignmentphylogeneticsreproducibleresearchsoftwarevisualizationannotationsggplot2phylogenetic-trees
864 stars 16.86 score 5.1k scripts 109 dependents
stan-dev
bayesplot:Plotting for Bayesian Models
Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow advocated in Gabry, Simpson, Vehtari, Betancourt, and Gelman (2019) <doi:10.1111/rssa.12378>. The package is designed not only to provide convenient functionality for users, but also a common set of functions that can be easily used by developers working on a variety of R packages for Bayesian modeling, particularly (but not exclusively) packages interfacing with 'Stan'.
Maintained by Jonah Gabry. Last updated 2 months ago.
bayesianggplot2mcmcpandocstanstatistical-graphicsvisualization
436 stars 16.69 score 6.5k scripts 98 dependents
jrnold
ggthemes:Extra Themes, Scales and Geoms for 'ggplot2'
Some extra themes, geoms, and scales for 'ggplot2'. Provides 'ggplot2' themes and scales that replicate the look of plots by Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata', 'Excel', and 'The Wall Street Journal', among others. Provides 'geoms' for Tufte's box plot and range frame.
Maintained by Jeffrey B. Arnold. Last updated 1 years ago.
data-visualisationggplot2ggplot2-themesplotplottingthemevisualization
1.3k stars 16.17 score 40k scripts 102 dependentsthomasp85
ggforce:Accelerating 'ggplot2'
The aim of 'ggplot2' is to aid in visual data investigations. This focus has led to a lack of facilities for composing specialised plots. 'ggforce' aims to be a collection of mainly new stats and geoms that fills this gap. All additional functionality is aimed to come through the official extension system so using 'ggforce' should be a stable experience.
Maintained by Thomas Lin Pedersen. Last updated 4 days ago.
ggplot-extensionggplot2visualizationcpp
929 stars 15.98 score 9.3k scripts 298 dependentsbioc
enrichplot:Visualization of Functional Enrichment Result
The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the 'clusterProfiler' package suite. All the visualization methods are developed based on 'ggplot2' graphics.
Maintained by Guangchuang Yu. Last updated 3 months ago.
annotationgenesetenrichmentgokeggpathwayssoftwarevisualizationenrichment-analysispathway-analysis
239 stars 15.71 score 3.1k scripts 58 dependents
hms-dbmi
UpSetR:A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
Creates visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks (Conway 2017) <doi:10.1093/bioinformatics/btx364>.
Maintained by Jake Conway. Last updated 4 years ago.
gehlenborglabggplot2upsetupsetrvisualization
781 stars 15.33 score 4.8k scripts 42 dependents
rich-iannone
DiagrammeR:Graph/Network Visualization
Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.
Maintained by Richard Iannone. Last updated 2 months ago.
graphgraph-functionsnetwork-graphproperty-graphvisualization
1.7k stars 15.29 score 3.8k scripts 86 dependentsbioc
DOSE:Disease Ontology Semantic and Enrichment analysis
This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.
Maintained by Guangchuang Yu. Last updated 5 months ago.
annotationvisualizationmultiplecomparisongenesetenrichmentpathwayssoftwaredisease-ontologyenrichment-analysissemantic-similarity
119 stars 14.97 score 2.0k scripts 61 dependents
mjskay
ggdist:Visualizations of Distributions and Uncertainty
Provides primitives for visualizing distributions using 'ggplot2' that are particularly tuned for visualizing uncertainty in either a frequentist or Bayesian mode. Both analytical distributions (such as frequentist confidence distributions or Bayesian priors) and distributions represented as samples (such as bootstrap distributions or Bayesian posterior samples) are easily visualized. Visualization primitives include but are not limited to: points with multiple uncertainty intervals, eye plots (Spiegelhalter D., 1999) <https://ideas.repec.org/a/bla/jorssa/v162y1999i1p45-58.html>, density plots, gradient plots, dot plots (Wilkinson L., 1999) <doi:10.1080/00031305.1999.10474474>, quantile dot plots (Kay M., Kola T., Hullman J., Munson S., 2016) <doi:10.1145/2858036.2858558>, complementary cumulative distribution function barplots (Fernandes M., Walls L., Munson S., Hullman J., Kay M., 2018) <doi:10.1145/3173574.3173718>, and fit curves with multiple uncertainty ribbons.
Maintained by Matthew Kay. Last updated 4 months ago.
ggplot2uncertaintyuncertainty-visualizationvisualizationcpp
859 stars 14.95 score 3.1k scripts 62 dependentsmjskay
tidybayes:Tidy Data and 'Geoms' for Bayesian Models
Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided to help extract tidy data frames of draws from Bayesian models and that generate point summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus densities), and fit curves with multiple, arbitrary uncertainty bands.
Maintained by Matthew Kay. Last updated 6 months ago.
bayesian-data-analysisbrmsggplot2jagsstantidy-datavisualization
733 stars 14.72 score 7.3k scripts 20 dependentsbioc
maftools:Summarize, Analyze and Visualize MAF Files
Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.
Maintained by Anand Mayakonda. Last updated 5 months ago.
datarepresentationdnaseqvisualizationdrivermutationvariantannotationfeatureextractionclassificationsomaticmutationsequencingfunctionalgenomicssurvivalbioinformaticscancer-genome-atlascancer-genomicsgenomicsmaf-filestcgacurlbzip2xz-utilszlib
459 stars 14.63 score 948 scripts 18 dependents
statistikat
VIM:Visualization and Imputation of Missing Values
New tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods. A graphical user interface available in the separate package VIMGUI allows an easy handling of the implemented plot methods.
Maintained by Matthias Templ. Last updated 8 months ago.
hotdeckimputation-methodsmodel-predictionsvisualizationcpp
85 stars 14.44 score 2.6k scripts 19 dependents
r-spatial
mapview:Interactive Viewing of Spatial Data in R
Quickly and conveniently create interactive visualisations of spatial data with or without background maps. Attributes of displayed features are fully queryable via pop-up windows. Additional functionality includes methods to visualise true- and false-color raster images and bounding boxes.
Maintained by Tim Appelhans. Last updated 3 months ago.
gisleafletmapsspatialvisualizationweb-mapping
526 stars 14.39 score 7.3k scripts 27 dependents
jbkunst
highcharter:A Wrapper for the 'Highcharts' Library
A wrapper for the 'Highcharts' library including shortcut functions to plot R objects. 'Highcharts' <https://www.highcharts.com/> is a charting library offering numerous chart types with a simple configuration syntax.
Maintained by Joshua Kunst. Last updated 1 years ago.
highchartshtmlwidgetsshinyshiny-rvisualizationwrapper
725 stars 13.93 score 4.9k scripts 18 dependents
hrbrmstr
hrbrthemes:Additional Themes, Theme Components and Utilities for 'ggplot2'
A compilation of extra 'ggplot2' themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography. A copy of the 'Google' font 'Roboto Condensed' is also included.
Maintained by Bob Rudis. Last updated 14 days ago.
data-visualizationdatavisualizationggplot-extensionggplot2ggplot2-scalesggplot2-themesvisualization
1.3k stars 13.92 score 13k scripts 15 dependents
knausb
vcfR:Manipulate and Visualize VCF Data
Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
Maintained by Brian J. Knaus. Last updated 1 months ago.
genomicspopulation-geneticspopulation-genomicsrcppvcf-datavisualizationzlibcpp
256 stars 13.66 score 3.1k scripts 19 dependentsbioc
RCy3:Functions to Access and Control Cytoscape
Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.
Maintained by Alex Pico. Last updated 2 days ago.
visualizationgraphandnetworkthirdpartyclientnetwork
52 stars 13.47 score 628 scripts 17 dependents
dreamrs
esquisse:Explore and Visualize Your Data Interactively
A 'shiny' gadget to create 'ggplot2' figures interactively with drag-and-drop to map your variables to different aesthetics. You can quickly visualize your data accordingly to their type, export in various formats, and retrieve the code to reproduce the plot.
Maintained by Victor Perrier. Last updated 1 months ago.
addindata-visualizationggplot2rstudio-addinvisualization
1.8k stars 13.31 score 1.1k scripts 1 dependents
easystats
see:Model Visualisation Toolbox for 'easystats' and 'ggplot2'
Provides plotting utilities supporting packages in the 'easystats' ecosystem (<https://github.com/easystats/easystats>) and some extra themes, geoms, and scales for 'ggplot2'. Color scales are based on <https://materialui.co/>. References: Lรผdecke et al. (2021) <doi:10.21105/joss.03393>.
Maintained by Indrajeet Patil. Last updated 17 days ago.
data-visualizationeasystatsggplot2hacktoberfestplottingseestatisticsvisualisationvisualization
902 stars 13.22 score 2.0k scripts 3 dependentsbioc
Gviz:Plotting data and annotation information along genomic coordinates
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
Maintained by Robert Ivanek. Last updated 5 months ago.
visualizationmicroarraysequencing
79 stars 13.08 score 1.4k scripts 48 dependentsbioc
ChIPseeker:ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.
Maintained by Guangchuang Yu. Last updated 5 months ago.
annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics
234 stars 13.02 score 1.6k scripts 5 dependentsbioc
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 23 days ago.
cellbasedassaysclusteringdimensionreductionfeatureextractiongeneexpressionguiimmunooncologyshinyappssinglecelltranscriptiontranscriptomicsvisualizationdimension-reductionfeature-extractiongene-expressionhacktoberfesthuman-cell-atlasshinysingle-cell
225 stars 12.86 score 380 scripts 9 dependentsbioc
EBImage:Image processing and analysis toolbox for R
EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.
Maintained by Andrzej Oleล. Last updated 5 months ago.
visualizationbioinformaticsimage-analysisimage-processingcpp
71 stars 12.77 score 1.5k scripts 33 dependentsbioc
rtracklayer:R interface to genome annotation files and the UCSC genome browser
Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
Maintained by Michael Lawrence. Last updated 3 days ago.
annotationvisualizationdataimportzlibopensslcurl
12.66 score 6.7k scripts 480 dependents
eliocamp
metR:Tools for Easier Analysis of Meteorological Fields
Many useful functions and extensions for dealing with meteorological data in the tidy data framework. Extends 'ggplot2' for better plotting of scalar and vector fields and provides commonly used analysis methods in the atmospheric sciences.
Maintained by Elio Campitelli. Last updated 9 days ago.
atmospheric-scienceggplot2visualization
146 stars 12.30 score 1000 scripts 22 dependentsbioc
ggbio:Visualization tools for genomic data
The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.
Maintained by Michael Lawrence. Last updated 5 months ago.
111 stars 12.26 score 734 scripts 17 dependentsbioc
ReactomePA:Reactome Pathway Analysis
This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. This package is not affiliated with the Reactome team.
Maintained by Guangchuang Yu. Last updated 5 months ago.
pathwaysvisualizationannotationmultiplecomparisongenesetenrichmentreactomeenrichment-analysisreactome-pathway-analysisreactomepa
40 stars 12.25 score 1.5k scripts 7 dependentsbioc
slingshot:Tools for ordering single-cell sequencing
Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.
Maintained by Kelly Street. Last updated 5 months ago.
clusteringdifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsvisualization
283 stars 12.01 score 1.0k scripts 4 dependents
stefanedwards
lemon:Freshing Up your 'ggplot2' Plots
Functions for working with legends and axis lines of 'ggplot2', facets that repeat axis lines on all panels, and some 'knitr' extensions.
Maintained by Stefan McKinnon Edwards. Last updated 5 months ago.
axis-linesfacetsggplot-extensionggplot2knitrlegendticksvisualization
190 stars 11.98 score 1.7k scripts 4 dependents
exaexa
scattermore:Scatterplots with More Points
C-based conversion of large scatterplot data to rasters plus other operations such as data blurring or data alpha blending. Speeds up plotting of data with millions of points.
Maintained by Mirek Kratochvil. Last updated 1 years ago.
performanceplotscatterplotvisualizationcpp
244 stars 11.95 score 596 scripts 85 dependents
guangchuangyu
hexSticker:Create Hexagon Sticker in R
Helper functions for creating reproducible hexagon sticker purely in R.
Maintained by Guangchuang Yu. Last updated 2 months ago.
ggplot2hexagon-stickerlogostickersvisualization
769 stars 11.94 score 1.3k scripts 8 dependentsbioc
metagenomeSeq:Statistical analysis for sparse high-throughput sequencing
metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.
Maintained by Joseph N. Paulson. Last updated 3 months ago.
immunooncologyclassificationclusteringgeneticvariabilitydifferentialexpressionmicrobiomemetagenomicsnormalizationvisualizationmultiplecomparisonsequencingsoftware
69 stars 11.90 score 494 scripts 7 dependents
rstudio
r2d3:Interface to 'D3' Visualizations
Suite of tools for using 'D3', a library for producing dynamic, interactive data visualizations. Supports translating objects into 'D3' friendly data structures, rendering 'D3' scripts, publishing 'D3' visualizations, incorporating 'D3' in R Markdown, creating interactive 'D3' applications with Shiny, and distributing 'D3' based 'htmlwidgets' in R packages.
Maintained by Nick Strayer. Last updated 3 years ago.
519 stars 11.88 score 498 scripts 10 dependentsbioc
methylKit:DNA methylation analysis from high-throughput bisulfite sequencing results
methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.
Maintained by Altuna Akalin. Last updated 28 days ago.
dnamethylationsequencingmethylseqgenome-biologymethylationstatistical-analysisvisualizationcurlbzip2xz-utilszlibcpp
220 stars 11.80 score 578 scripts 3 dependents
bgreenwell
pdp:Partial Dependence Plots
A general framework for constructing partial dependence (i.e., marginal effect) plots from various types machine learning models in R.
Maintained by Brandon M. Greenwell. Last updated 3 years ago.
black-box-modelmachine-learningpartial-dependence-functionpartial-dependence-plotvisualization
93 stars 11.72 score 1.1k scripts 8 dependents
jbryer
likert:Analysis and Visualization Likert Items
An approach to analyzing Likert response items, with an emphasis on visualizations. The stacked bar plot is the preferred method for presenting Likert results. Tabular results are also implemented along with density plots to assist researchers in determining whether Likert responses can be used quantitatively instead of qualitatively. See the likert(), summary.likert(), and plot.likert() functions to get started.
Maintained by Jason Bryer. Last updated 3 days ago.
310 stars 11.71 score 480 scripts 2 dependentsbioc
Rgraphviz:Provides plotting capabilities for R graph objects
Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.
Maintained by Kasper Daniel Hansen. Last updated 2 days ago.
graphandnetworkvisualizationzlib
11.51 score 1.2k scripts 107 dependents
johncoene
echarts4r:Create Interactive Graphs with 'Echarts JavaScript' Version 5
Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 36 chart types, themes, 'Shiny' proxies and animations.
Maintained by David Munoz Tord. Last updated 15 days ago.
echartshacktoberfesthtmlwidgethtmlwidgetsvisualization
603 stars 11.45 score 1.3k scripts 11 dependentsbioc
destiny:Creates diffusion maps
Create and plot diffusion maps.
Maintained by Philipp Angerer. Last updated 4 months ago.
cellbiologycellbasedassaysclusteringsoftwarevisualizationdiffusion-mapsdimensionality-reductioncpp
82 stars 11.44 score 792 scripts 1 dependents
lazappi
clustree:Visualise Clusterings at Different Resolutions
Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.
Maintained by Luke Zappia. Last updated 1 years ago.
clusteringclustering-treesvisualisationvisualization
219 stars 11.40 score 1.9k scripts 5 dependents
neuhausi
canvasXpress:Visualization Package for CanvasXpress in R
Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <https://www.canvasxpress.org> for more information.
Maintained by Connie Brett. Last updated 10 hours ago.
analyticsbioinformaticschartchartingdashdashboarddata-analyticsdata-sciencedata-visualizationgenomicsgraphsjavascriptnetworknetwork-visualizationpythonreproducible-researchshinyvisualization
297 stars 11.28 score 145 scriptsbioc
ggcyto:Visualize Cytometry data with ggplot
With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.
Maintained by Mike Jiang. Last updated 5 months ago.
immunooncologyflowcytometrycellbasedassaysinfrastructurevisualization
58 stars 11.25 score 362 scripts 5 dependentsbioc
pathview:a tool set for pathway based data integration and visualization
Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.
Maintained by Weijun Luo. Last updated 5 months ago.
pathwaysgraphandnetworkvisualizationgenesetenrichmentdifferentialexpressiongeneexpressionmicroarrayrnaseqgeneticsmetabolomicsproteomicssystemsbiologysequencing
40 stars 11.24 score 1.6k scripts 10 dependentsbioc
karyoploteR:Plot customizable linear genomes displaying arbitrary data
karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.
Maintained by Bernat Gel. Last updated 5 months ago.
visualizationcopynumbervariationsequencingcoveragednaseqchipseqmethylseqdataimportonechannelbioconductorbioinformaticsdata-visualizationgenomegenomics-visualizationplotting-in-r
306 stars 11.22 score 656 scripts 4 dependents
boxuancui
DataExplorer:Automate Data Exploration and Treatment
Automated data exploration process for analytic tasks and predictive modeling, so that users could focus on understanding data and extracting insights. The package scans and analyzes each variable, and visualizes them with typical graphical techniques. Common data processing methods are also available to treat and format data.
Maintained by Boxuan Cui. Last updated 1 years ago.
data-analysisdata-explorationdata-scienceedavisualization
523 stars 11.21 score 2.2k scriptsguangchuangyu
ggimage:Use Image in 'ggplot2'
Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.
Maintained by Guangchuang Yu. Last updated 1 years ago.
172 stars 11.16 score 2.4k scripts 20 dependentsbioc
genomation:Summary, annotation and visualization of genomic data
A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.
Maintained by Altuna Akalin. Last updated 5 months ago.
annotationsequencingvisualizationcpgislandcpp
75 stars 11.09 score 738 scripts 5 dependentsbioc
scater:Single-Cell Analysis Toolkit for Gene Expression Data in R
A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.
Maintained by Alan OCallaghan. Last updated 22 days ago.
immunooncologysinglecellrnaseqqualitycontrolpreprocessingnormalizationvisualizationdimensionreductiontranscriptomicsgeneexpressionsequencingsoftwaredataimportdatarepresentationinfrastructurecoverage
11.07 score 12k scripts 43 dependentsbioc
CATALYST:Cytometry dATa anALYSis Tools
CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively.
Maintained by Helena L. Crowell. Last updated 4 months ago.
clusteringdataimportdifferentialexpressionexperimentaldesignflowcytometryimmunooncologymassspectrometrynormalizationpreprocessingsinglecellsoftwarestatisticalmethodvisualization
67 stars 11.06 score 362 scripts 2 dependents
mhahsler
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 dependents
cpsievert
LDAvis:Interactive Visualization of Topic Models
Tools to create an interactive web-based visualization of a topic model that has been fit to a corpus of text data using Latent Dirichlet Allocation (LDA). Given the estimated parameters of the topic model, it computes various summary statistics as input to an interactive visualization built with 'D3.js' that is accessed via a browser. The goal is to help users interpret the topics in their 'LDA' topic model.
Maintained by Carson Sievert. Last updated 7 years ago.
javascripttext-miningtopic-modelingvisualization
558 stars 10.93 score 804 scripts 1 dependentsbioc
EnrichedHeatmap:Making Enriched Heatmaps
Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.
Maintained by Zuguang Gu. Last updated 5 months ago.
softwarevisualizationsequencinggenomeannotationcoveragecpp
190 stars 10.87 score 330 scripts 1 dependentsthomasp85
scico:Colour Palettes Based on the Scientific Colour-Maps
Colour choice in information visualisation is important in order to avoid being mislead by inherent bias in the used colour palette. The 'scico' package provides access to the perceptually uniform and colour-blindness friendly palettes developed by Fabio Crameri and released under the "Scientific Colour-Maps" moniker. The package contains 24 different palettes and includes both diverging and sequential types.
Maintained by Thomas Lin Pedersen. Last updated 2 years ago.
444 stars 10.80 score 2.0k scripts 7 dependents
erocoar
gghalves:Compose Half-Half Plots Using Your Favourite Geoms
A 'ggplot2' extension for easy plotting of half-half geom combinations. Think half boxplot and half jitterplot, or half violinplot and half dotplot.
Maintained by Frederik Tiedemann. Last updated 2 years ago.
datavizggplot-extensionggplot2visualization
243 stars 10.78 score 872 scripts 7 dependents
rempsyc
rempsyc:Convenience Functions for Psychology
Make your workflow faster and easier. Easily customizable plots (via 'ggplot2'), nice APA tables (following the style of the *American Psychological Association*) exportable to Word (via 'flextable'), easily run statistical tests or check assumptions, and automatize various other tasks.
Maintained by Rรฉmi Thรฉriault. Last updated 2 months ago.
convenience-functionsggplot2psychologystatisticsvisualization
43 stars 10.68 score 214 scripts 2 dependentsbioc
Glimma:Interactive visualizations for gene expression analysis
This package produces interactive visualizations for RNA-seq data analysis, utilizing output from limma, edgeR, or DESeq2. It produces interactive htmlwidgets versions of popular RNA-seq analysis plots to enhance the exploration of analysis results by overlaying interactive features. The plots can be viewed in a web browser or embedded in notebook documents.
Maintained by Shian Su. Last updated 2 months ago.
differentialexpressiongeneexpressionmicroarrayreportwritingrnaseqsequencingvisualizationdifferential-expressioninteractive-visualizations
32 stars 10.58 score 600 scripts 1 dependentsbioc
DECIPHER:Tools for curating, analyzing, and manipulating biological sequences
A toolset for deciphering and managing biological sequences.
Maintained by Erik Wright. Last updated 17 days ago.
clusteringgeneticssequencingdataimportvisualizationmicroarrayqualitycontrolqpcralignmentwholegenomemicrobiomeimmunooncologygenepredictionopenmp
10.55 score 1.1k scripts 14 dependents
willgearty
deeptime:Plotting Tools for Anyone Working in Deep Time
Extends the functionality of other plotting packages (notably 'ggplot2') to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of 'deeptime' is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.
Maintained by William Gearty. Last updated 3 months ago.
geologyggplot2paleontologyvisualization
92 stars 10.46 score 207 scripts 3 dependentsbioc
ChemmineR:Cheminformatics Toolkit for R
ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.
Maintained by Thomas Girke. Last updated 5 months ago.
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp
15 stars 10.45 score 253 scripts 12 dependentsbioc
muscat:Multi-sample multi-group scRNA-seq data analysis tools
`muscat` provides various methods and visualization tools for DS analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated โpseudobulkโ data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.
Maintained by Helena L. Crowell. Last updated 5 months ago.
immunooncologydifferentialexpressionsequencingsinglecellsoftwarestatisticalmethodvisualization
181 stars 10.26 score 686 scriptsbioc
plotgardener:Coordinate-Based Genomic Visualization Package for R
Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.
Maintained by Nicole Kramer. Last updated 5 months ago.
visualizationgenomeannotationfunctionalgenomicsgenomeassemblyhiccpp
309 stars 10.17 score 167 scripts 3 dependentsbioc
SC3:Single-Cell Consensus Clustering
A tool for unsupervised clustering and analysis of single cell RNA-Seq data.
Maintained by Vladimir Kiselev. Last updated 5 months ago.
immunooncologysinglecellsoftwareclassificationclusteringdimensionreductionsupportvectormachinernaseqvisualizationtranscriptomicsdatarepresentationguidifferentialexpressiontranscriptionbioconductor-packagehuman-cell-atlassingle-cell-rna-seqopenblascpp
125 stars 10.10 score 374 scripts 1 dependents
modeloriented
shapviz:SHAP Visualizations
Visualizations for SHAP (SHapley Additive exPlanations), such as waterfall plots, force plots, various types of importance plots, dependence plots, and interaction plots. These plots act on a 'shapviz' object created from a matrix of SHAP values and a corresponding feature dataset. Wrappers for the R packages 'xgboost', 'lightgbm', 'fastshap', 'shapr', 'h2o', 'treeshap', 'DALEX', and 'kernelshap' are added for convenience. By separating visualization and computation, it is possible to display factor variables in graphs, even if the SHAP values are calculated by a model that requires numerical features. The plots are inspired by those provided by the 'shap' package in Python, but there is no dependency on it.
Maintained by Michael Mayer. Last updated 2 months ago.
explainable-aimachine-learningshapshapley-valuevisualizationxai
90 stars 10.07 score 250 scriptsbioc
tradeSeq:trajectory-based differential expression analysis for sequencing data
tradeSeq provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.
Maintained by Hector Roux de Bezieux. Last updated 5 months ago.
clusteringregressiontimecoursedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization
251 stars 10.06 score 440 scriptsbioc
MOFA2:Multi-Omics Factor Analysis v2
The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available.
Maintained by Ricard Argelaguet. Last updated 5 months ago.
dimensionreductionbayesianvisualizationfactor-analysismofamulti-omics
319 stars 10.02 score 502 scripts
timelyportfolio
sunburstR:Sunburst 'Htmlwidget'
Make interactive 'd3.js' sequence sunburst diagrams in R with the convenience and infrastructure of an 'htmlwidget'.
Maintained by Kent Russell. Last updated 2 years ago.
chartd3htmlwidgetsinteractivejavascriptvisualization
210 stars 10.02 score 310 scripts 4 dependents
laresbernardo
lares:Analytics & Machine Learning Sidekick
Auxiliary package for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling, Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or advanced R programming skills.
Maintained by Bernardo Lares. Last updated 1 months ago.
analyticsapiautomationautomldata-sciencedescriptive-statisticsh2omachine-learningmarketingmmmpredictive-modelingpuzzlerlanguagerobynvisualization
233 stars 9.92 score 185 scripts 1 dependents
hafen
geofacet:'ggplot2' Faceting Utilities for Geographical Data
Provides geographical faceting functionality for 'ggplot2'. Geographical faceting arranges a sequence of plots of data for different geographical entities into a grid that preserves some of the geographical orientation.
Maintained by Ryan Hafen. Last updated 7 months ago.
339 stars 9.79 score 1.5k scripts 4 dependentsbioc
annotatr:Annotation of Genomic Regions to Genomic Annotations
Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.
Maintained by Raymond G. Cavalcante. Last updated 5 months ago.
softwareannotationgenomeannotationfunctionalgenomicsvisualizationgenome-annotation
26 stars 9.76 score 246 scripts 5 dependentsbioc
MicrobiotaProcess:A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).
Maintained by Shuangbin Xu. Last updated 5 months ago.
visualizationmicrobiomesoftwaremultiplecomparisonfeatureextractionmicrobiome-analysismicrobiome-data
183 stars 9.70 score 126 scripts 1 dependentsbioc
InteractiveComplexHeatmap:Make Interactive Complex Heatmaps
This package can easily make heatmaps which are produced by the ComplexHeatmap package into interactive applications. It provides two types of interactivities: 1. on the interactive graphics device, and 2. on a Shiny app. It also provides functions for integrating the interactive heatmap widgets for more complex Shiny app development.
Maintained by Zuguang Gu. Last updated 5 months ago.
softwarevisualizationsequencinginteractive-heatmaps
132 stars 9.69 score 128 scripts 4 dependentsbioc
Nebulosa:Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation
This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). Seurat and SingleCellExperiment objects can be used within Nebulosa.
Maintained by Jose Alquicira-Hernandez. Last updated 5 months ago.
softwaregeneexpressionsinglecellvisualizationdimensionreductionsingle-cellsingle-cell-analysissingle-cell-multiomicssingle-cell-rna-seq
99 stars 9.66 score 494 scriptsbioc
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 scriptshafen
trelliscopejs:Create Interactive Trelliscope Displays
Trelliscope is a scalable, flexible, interactive approach to visualizing data (Hafen, 2013 <doi:10.1109/LDAV.2013.6675164>). This package provides methods that make it easy to create a Trelliscope display specification for TrelliscopeJS. High-level functions are provided for creating displays from within 'tidyverse' or 'ggplot2' workflows. Low-level functions are also provided for creating new interfaces.
Maintained by Ryan Hafen. Last updated 1 years ago.
262 stars 9.61 score 1000 scripts 1 dependentsbioc
ggtreeExtra:An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
'ggtreeExtra' extends the method for mapping and visualizing associated data on phylogenetic tree using 'ggtree'. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by 'ggtree' with the grammar of 'ggplot2'.
Maintained by Shuangbin Xu. Last updated 5 months ago.
softwarevisualizationphylogeneticsannotation
91 stars 9.55 score 426 scripts 2 dependents
krassowski
ComplexUpset:Create Complex UpSet Plots Using 'ggplot2' Components
UpSet plots are an improvement over Venn Diagram for set overlap visualizations. Striving to bring the best of the 'UpSetR' and 'ggplot2', this package offers a way to create complex overlap visualisations, using simple and familiar tools, i.e. geoms of 'ggplot2'. For introduction to UpSet concept, see Lex et al. (2014) <doi:10.1109/TVCG.2014.2346248>.
Maintained by Michaล Krassowski. Last updated 1 years ago.
ggplotggplot2patchworkpythonrstatupsetupsetrvennvenn-diagramvisualization
491 stars 9.54 score 554 scripts 4 dependents
dcousin3
superb:Summary Plots with Adjusted Error Bars
Computes standard error and confidence interval of various descriptive statistics under various designs and sampling schemes. The main function, superb(), return a plot. It can also be used to obtain a dataframe with the statistics and their precision intervals so that other plotting environments (e.g., Excel) can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109> or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005) <doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012) <doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>, Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding <doi:10.20982/tqmp.15.1.p001> for specific references.
Maintained by Denis Cousineau. Last updated 2 months ago.
error-barsplottingstatisticssummary-plotssummary-statisticsvisualization
19 stars 9.53 score 155 scripts 2 dependents
shixiangwang
sigminer:Extract, Analyze and Visualize Mutational Signatures for Genomic Variations
Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al. (2022) <DOI:10.1038/s41586-022-04738-6>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
Maintained by Shixiang Wang. Last updated 6 months ago.
bayesian-nmfbioinformaticscancer-researchcnvcopynumber-signaturescosmic-signaturesdbseasy-to-useindelmutational-signaturesnmfnmf-extractionsbssignature-extractionsomatic-mutationssomatic-variantsvisualizationcpp
150 stars 9.48 score 123 scripts 2 dependents
mlr-org
mlr3viz:Visualizations for 'mlr3'
Visualization package of the 'mlr3' ecosystem. It features plots for mlr3 objects such as tasks, learners, predictions, benchmark results, tuning instances and filters via the 'autoplot()' generic of 'ggplot2'. The package draws plots with the 'viridis' color palette and applies the minimal theme. Visualizations include barplots, boxplots, histograms, ROC curves, and Precision-Recall curves.
Maintained by Marc Becker. Last updated 5 months ago.
ggplot2mlr3visualizationvisualizations
45 stars 9.45 score 364 scripts 4 dependentsbioc
DEGreport:Report of DEG analysis
Creation of ready-to-share figures of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.
Maintained by Lorena Pantano. Last updated 5 months ago.
differentialexpressionvisualizationrnaseqreportwritinggeneexpressionimmunooncologybioconductordifferential-expressionqcreportrna-seqsmallrna
24 stars 9.42 score 354 scripts 1 dependentsbioc
ggmsa:Plot Multiple Sequence Alignment using 'ggplot2'
A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using 'ggplot2'. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as phylogenetic tree Visualized by 'ggtree', boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.
Maintained by Guangchuang Yu. Last updated 3 months ago.
softwarevisualizationalignmentannotationmultiplesequencealignment
210 stars 9.35 score 196 scripts 2 dependents
lkremer
ggpointdensity:A Cross Between a 2D Density Plot and a Scatter Plot
A cross between a 2D density plot and a scatter plot, implemented as a 'ggplot2' geom. Points in the scatter plot are colored by the number of neighboring points. This is useful to visualize the 2D-distribution of points in case of overplotting.
Maintained by Lukas P. M. Kremer. Last updated 11 months ago.
2d-density-plotdensity-visualizationgeomggplot-extensionggplot2ggplot2-enhancementsggplot2-geomsneighboring-pointsscatter-plotvisualization
424 stars 9.30 score 1.1k scripts 4 dependentsbioc
EWCE:Expression Weighted Celltype Enrichment
Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.
Maintained by Alan Murphy. Last updated 1 months ago.
geneexpressiontranscriptiondifferentialexpressiongenesetenrichmentgeneticsmicroarraymrnamicroarrayonechannelrnaseqbiomedicalinformaticsproteomicsvisualizationfunctionalgenomicssinglecelldeconvolutionsingle-cellsingle-cell-rna-seqtranscriptomics
56 stars 9.29 score 99 scriptsbioc
CNEr:CNE Detection and Visualization
Large-scale identification and advanced visualization of sets of conserved noncoding elements.
Maintained by Ge Tan. Last updated 5 months ago.
generegulationvisualizationdataimport
3 stars 9.28 score 35 scripts 19 dependentsbioc
IsoformSwitchAnalyzeR:Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data
Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.
Maintained by Kristoffer Vitting-Seerup. Last updated 5 months ago.
geneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicingvisualizationstatisticalmethodtranscriptomevariantbiomedicalinformaticsfunctionalgenomicssystemsbiologytranscriptomicsrnaseqannotationfunctionalpredictiongenepredictiondataimportmultiplecomparisonbatcheffectimmunooncology
108 stars 9.26 score 125 scriptsbioc
rWikiPathways:rWikiPathways - R client library for the WikiPathways API
Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.
Maintained by Egon Willighagen. Last updated 5 months ago.
visualizationgraphandnetworkthirdpartyclientnetworkmetabolomicsbioinformaticsdata-accesspathways
15 stars 9.23 score 131 scripts 3 dependentsbioc
BatchQC:Batch Effects Quality Control Software
Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. BatchQC is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. BatchQC diagnostics help determine whether batch adjustment needs to be done, and how correction should be applied before proceeding with a downstream analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches to the data and the user can quickly see the benefits of each method. BatchQC is developed as a Shiny App. The output is organized into multiple tabs and each tab features an important part of the batch effect analysis and visualization of the data. The BatchQC interface has the following analysis groups: Summary, Differential Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.
Maintained by Jessica Anderson. Last updated 10 days ago.
batcheffectgraphandnetworkmicroarraynormalizationprincipalcomponentsequencingsoftwarevisualizationqualitycontrolrnaseqpreprocessingdifferentialexpressionimmunooncology
7 stars 9.06 score 54 scripts
ramikrispin
TSstudio:Functions for Time Series Analysis and Forecasting
Provides a set of tools for descriptive and predictive analysis of time series data. That includes functions for interactive visualization of time series objects and as well utility functions for automation time series forecasting.
Maintained by Rami Krispin. Last updated 2 years ago.
forecastingtime-seriestimeseriestsstudiovisualization
425 stars 9.02 score 656 scriptsbioc
scPipe:Pipeline for single cell multi-omic data pre-processing
A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.
Maintained by Shian Su. Last updated 3 months ago.
immunooncologysoftwaresequencingrnaseqgeneexpressionsinglecellvisualizationsequencematchingpreprocessingqualitycontrolgenomeannotationdataimportcurlbzip2xz-utilszlibcpp
68 stars 9.02 score 84 scripts
friendly
candisc:Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis
Functions for computing and visualizing generalized canonical discriminant analyses and canonical correlation analysis for a multivariate linear model. Traditional canonical discriminant analysis is restricted to a one-way 'MANOVA' design and is equivalent to canonical correlation analysis between a set of quantitative response variables and a set of dummy variables coded from the factor variable. The 'candisc' package generalizes this to higher-way 'MANOVA' designs for all factors in a multivariate linear model, computing canonical scores and vectors for each term. The graphic functions provide low-rank (1D, 2D, 3D) visualizations of terms in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Related plots are now provided for canonical correlation analysis when all predictors are quantitative.
Maintained by Michael Friendly. Last updated 1 days ago.
dimension-reductionmultivariate-linear-modelsvisualization
15 stars 8.99 score 221 scripts 3 dependentsbioc
schex:Hexbin plots for single cell omics data
Builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment. The ideas used in this package are based on the excellent work of Dan Carr, Nicholas Lewin-Koh, Martin Maechler and Thomas Lumley.
Maintained by Saskia Freytag. Last updated 5 months ago.
softwaresequencingsinglecelldimensionreductionvisualizationimmunooncologydataimport
74 stars 8.96 score 102 scripts 2 dependentsbioc
topGO:Enrichment Analysis for Gene Ontology
topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
Maintained by Adrian Alexa. Last updated 5 months ago.
8.96 score 2.0k scripts 20 dependentsbioc
RTCGA:The Cancer Genome Atlas Data Integration
The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.
Maintained by Marcin Kosinski. Last updated 5 months ago.
immunooncologysoftwaredataimportdatarepresentationpreprocessingrnaseqsurvivaldnamethylationprincipalcomponentvisualization
51 stars 8.91 score 106 scripts 1 dependentsbioc
motifbreakR:A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 32 species, a total of 109 versions).
Maintained by Simon Gert Coetzee. Last updated 5 months ago.
chipseqvisualizationmotifannotationtranscription
28 stars 8.89 score 103 scriptsbioc
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
scmap:A tool for unsupervised projection of single cell RNA-seq data
Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment on to the cell-types or individual cells identified in a different experiment.
Maintained by Vladimir Kiselev. Last updated 5 months ago.
immunooncologysinglecellsoftwareclassificationsupportvectormachinernaseqvisualizationtranscriptomicsdatarepresentationtranscriptionsequencingpreprocessinggeneexpressiondataimportbioconductor-packagehuman-cell-atlasprojection-mappingsingle-cell-rna-seqopenblascpp
95 stars 8.82 score 172 scriptsbioc
drawProteins:Package to Draw Protein Schematics from Uniprot API output
This package draws protein schematics from Uniprot API output. From the JSON returned by the GET command, it creates a dataframe from the Uniprot Features API. This dataframe can then be used by geoms based on ggplot2 and base R to draw protein schematics.
Maintained by Paul Brennan. Last updated 5 months ago.
visualizationfunctionalpredictionproteomics
34 stars 8.75 score 61 scripts 1 dependents
enblacar
SCpubr:Generate Publication Ready Visualizations of Single Cell Transcriptomics Data
A system that provides a streamlined way of generating publication ready plots for known Single-Cell transcriptomics data in a โpublication readyโ format. This is, the goal is to automatically generate plots with the highest quality possible, that can be used right away or with minimal modifications for a research article.
Maintained by Enrique Blanco-Carmona. Last updated 1 months ago.
softwaresinglecellvisualizationdata-visualizationggplot2publication-quality-plotsseuratsingle-cellsingle-cell-genomicssingle-cell-rna-seq
178 stars 8.71 score 194 scriptsbioc
Voyager:From geospatial to spatial omics
SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results.
Maintained by Lambda Moses. Last updated 3 months ago.
geneexpressionspatialtranscriptomicsvisualizationbioconductoredaesdaexploratory-data-analysisomicsspatial-statisticsspatial-transcriptomics
88 stars 8.71 score 173 scriptsbioc
monocle:Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.
Maintained by Cole Trapnell. Last updated 5 months ago.
immunooncologysequencingrnaseqgeneexpressiondifferentialexpressioninfrastructuredataimportdatarepresentationvisualizationclusteringmultiplecomparisonqualitycontrolcpp
8.71 score 1.6k scripts 2 dependentsbioc
trackViewer:A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.
Maintained by Jianhong Ou. Last updated 3 months ago.
8.71 score 145 scripts 2 dependentsbioc
miaViz:Microbiome Analysis Plotting and Visualization
The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.
Maintained by Tuomas Borman. Last updated 9 days ago.
microbiomesoftwarevisualizationbioconductormicrobiome-analysisplotting
10 stars 8.67 score 81 scripts 1 dependents
nowosad
rcartocolor:'CARTOColors' Palettes
Provides color schemes for maps and other graphics designed by 'CARTO' as described at <https://carto.com/carto-colors/>. It includes four types of palettes: aggregation, diverging, qualitative, and quantitative.
Maintained by Jakub Nowosad. Last updated 6 months ago.
color-paletteggplot2visualization
111 stars 8.64 score 1.4k scripts 1 dependentsbioc
HiCcompare:HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.
Maintained by Mikhail Dozmorov. Last updated 5 months ago.
softwarehicsequencingnormalizationdifference-detectionhi-cvisualization
19 stars 8.61 score 51 scripts 5 dependentsbioc
SPIAT:Spatial Image Analysis of Tissues
SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.
Maintained by Yuzhou Feng. Last updated 13 days ago.
biomedicalinformaticscellbiologyspatialclusteringdataimportimmunooncologyqualitycontrolsinglecellsoftwarevisualization
22 stars 8.59 score 69 scriptsguangchuangyu
emojifont:Emoji and Font Awesome in Graphics
An implementation of using emoji and fontawesome for using in both base and 'ggplot2' graphics.
Maintained by Guangchuang Yu. Last updated 4 years ago.
emojifont-awesomeggplot2visualization
67 stars 8.47 score 900 scripts 3 dependentsbioc
survcomp:Performance Assessment and Comparison for Survival Analysis
Assessment and Comparison for Performance of Risk Prediction (Survival) Models.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
geneexpressiondifferentialexpressionvisualizationcpp
8.46 score 448 scripts 12 dependents
samuel-marsh
scCustomize:Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Maintained by Samuel Marsh. Last updated 3 months ago.
customizationggplot2scrna-seqseuratsingle-cellsingle-cell-genomicssingle-cell-rna-seqvisualization
246 stars 8.45 score 1.1k scripts
ewenme
ghibli:Studio Ghibli Colour Palettes
Colour palettes inspired by Studio Ghibli <https://en.wikipedia.org/wiki/Studio_Ghibli> films, ported to R for your enjoyment.
Maintained by Ewen Henderson. Last updated 1 years ago.
ggplot2ghiblipalettevisualization
427 stars 8.44 score 324 scripts
davidhodge931
ggblanket:Simplify 'ggplot2' Visualisation
Simplify 'ggplot2' visualisation with 'ggblanket' wrapper functions.
Maintained by David Hodge. Last updated 10 days ago.
data-visualisationdata-visualizationggplotggplot-extensionggplot2ggplot2-enhancementsvisualisationvisualization
173 stars 8.42 score 45 scriptsbioc
geneplotter:Graphics related functions for Bioconductor
Functions for plotting genomic data
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
8.40 score 249 scripts 10 dependentsbioc
EnrichmentBrowser:Seamless navigation through combined results of set-based and network-based enrichment analysis
The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.
Maintained by Ludwig Geistlinger. Last updated 5 months ago.
immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwriting
20 stars 8.37 score 164 scripts 3 dependentsbioc
igvR:igvR: integrative genomics viewer
Access to igv.js, the Integrative Genomics Viewer running in a web browser.
Maintained by Arkadiusz Gladki. Last updated 5 months ago.
visualizationthirdpartyclientgenomebrowsers
45 stars 8.33 score 118 scriptsbioc
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 dependents
rrrlw
TDAstats:Pipeline for Topological Data Analysis
A comprehensive toolset for any useR conducting topological data analysis, specifically via the calculation of persistent homology in a Vietoris-Rips complex. The tools this package currently provides can be conveniently split into three main sections: (1) calculating persistent homology; (2) conducting statistical inference on persistent homology calculations; (3) visualizing persistent homology and statistical inference. The published form of TDAstats can be found in Wadhwa et al. (2018) <doi:10.21105/joss.00860>. For a general background on computing persistent homology for topological data analysis, see Otter et al. (2017) <doi:10.1140/epjds/s13688-017-0109-5>. To learn more about how the permutation test is used for nonparametric statistical inference in topological data analysis, read Robinson & Turner (2017) <doi:10.1007/s41468-017-0008-7>. To learn more about how TDAstats calculates persistent homology, you can visit the GitHub repository for Ripser, the software that works behind the scenes at <https://github.com/Ripser/ripser>. This package has been published as Wadhwa et al. (2018) <doi:10.21105/joss.00860>.
Maintained by Raoul Wadhwa. Last updated 3 years ago.
data-scienceggplot2homologyhomology-calculationshomology-computationjosspersistent-homologypipelineripsertdatopological-data-analysistopologytopology-visualizationvisualizationcpp
40 stars 8.30 score 46 scripts 4 dependentsbioc
GeneTonic:Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.
Maintained by Federico Marini. Last updated 3 months ago.
guigeneexpressionsoftwaretranscriptiontranscriptomicsvisualizationdifferentialexpressionpathwaysreportwritinggenesetenrichmentannotationgoshinyappsbioconductorbioconductor-packagedata-explorationdata-visualizationfunctional-enrichment-analysisgene-expressionpathway-analysisreproducible-researchrna-seq-analysisrna-seq-datashinytranscriptomeuser-friendly
77 stars 8.28 score 37 scripts 1 dependentsbioc
gtrellis:Genome Level Trellis Layout
Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.
Maintained by Zuguang Gu. Last updated 5 months ago.
softwarevisualizationsequencing
39 stars 8.24 score 37 scripts 1 dependentsbioc
nullranges:Generation of null ranges via bootstrapping or covariate matching
Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.
Maintained by Michael Love. Last updated 5 months ago.
visualizationgenesetenrichmentfunctionalgenomicsepigeneticsgeneregulationgenetargetgenomeannotationannotationgenomewideassociationhistonemodificationchipseqatacseqdnaseseqrnaseqhiddenmarkovmodelbioconductorbootstrapgenomicsmatchingstatistics
27 stars 8.16 score 50 scripts 1 dependentsbioc
POMA:Tools for Omics Data Analysis
The POMA package offers a comprehensive toolkit designed for omics data analysis, streamlining the process from initial visualization to final statistical analysis. Its primary goal is to simplify and unify the various steps involved in omics data processing, making it more accessible and manageable within a single, intuitive R package. Emphasizing on reproducibility and user-friendliness, POMA leverages the standardized SummarizedExperiment class from Bioconductor, ensuring seamless integration and compatibility with a wide array of Bioconductor tools. This approach guarantees maximum flexibility and replicability, making POMA an essential asset for researchers handling omics datasets. See https://github.com/pcastellanoescuder/POMAShiny. Paper: Castellano-Escuder et al. (2021) <doi:10.1371/journal.pcbi.1009148> for more details.
Maintained by Pol Castellano-Escuder. Last updated 4 months ago.
batcheffectclassificationclusteringdecisiontreedimensionreductionmultidimensionalscalingnormalizationpreprocessingprincipalcomponentregressionrnaseqsoftwarestatisticalmethodvisualizationbioconductorbioinformaticsdata-visualizationdimension-reductionexploratory-data-analysismachine-learningomics-data-integrationpipelinepre-processingstatistical-analysisuser-friendlyworkflow
11 stars 8.16 score 20 scripts 1 dependentsbioc
ggkegg:Analyzing and visualizing KEGG information using the grammar of graphics
This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.
Maintained by Noriaki Sato. Last updated 2 months ago.
pathwaysdataimportkeggggplot2ggraphpathwaytidygraphvisualization
224 stars 8.12 score 30 scripts 1 dependentsbioc
monaLisa:Binned Motif Enrichment Analysis and Visualization
Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.
Maintained by Michael Stadler. Last updated 5 days ago.
motifannotationvisualizationfeatureextractionepigenetics
40 stars 8.10 score 53 scripts
sportsdataverse
sportyR:Plot Scaled 'ggplot' Representations of Sports Playing Surfaces
Create scaled 'ggplot' representations of playing surfaces. Playing surfaces are drawn pursuant to rule-book specifications. This package should be used as a baseline plot for displaying any type of tracking data.
Maintained by Ross Drucker. Last updated 2 months ago.
footballggplot2playing-surfacessportsports-analyticssports-datasports-tracking-datasportsdataversevisualization
104 stars 8.08 score 97 scripts
cbailiss
pivottabler:Create Pivot Tables
Create regular pivot tables with just a few lines of R. More complex pivot tables can also be created, e.g. pivot tables with irregular layouts, multiple calculations and/or derived calculations based on multiple data frames. Pivot tables are constructed using R only and can be written to a range of output formats (plain text, 'HTML', 'Latex' and 'Excel'), including with styling/formatting.
Maintained by Christopher Bailiss. Last updated 1 years ago.
calculationshtmlhtmlwidgetlatexpivot-tablesvisualization
122 stars 8.08 score 358 scripts 1 dependents
predictiveecology
quickPlot:A System of Plotting Optimized for Speed and Modularity
A high-level plotting system, compatible with `ggplot2` objects, maps from `sf`, `terra`, `raster`, `sp`. It is built primarily on the 'grid' package. The objective of the package is to provide a plotting system that is built for speed and modularity. This is useful for quick visualizations when testing code and for plotting multiple figures to the same device from independent sources that may be independent of one another (i.e., different function or modules the create the visualizations). The suggested package 'fastshp' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).
Maintained by Eliot J B McIntire. Last updated 4 months ago.
6 stars 8.08 score 121 scripts 12 dependentsbioc
biovizBase:Basic graphic utilities for visualization of genomic data.
The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.
Maintained by Michael Lawrence. Last updated 5 months ago.
infrastructurevisualizationpreprocessing
8.03 score 273 scripts 74 dependentsbioc
simplifyEnrichment:Simplify Functional Enrichment Results
A new clustering algorithm, "binary cut", for clustering similarity matrices of functional terms is implemeted in this package. It also provides functions for visualizing, summarizing and comparing the clusterings.
Maintained by Zuguang Gu. Last updated 5 months ago.
softwarevisualizationgoclusteringgenesetenrichment
113 stars 8.02 score 196 scriptsbioc
motifStack:Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.
Maintained by Jianhong Ou. Last updated 3 months ago.
sequencematchingvisualizationsequencingmicroarrayalignmentchipchipchipseqmotifannotationdataimport
7.93 score 188 scripts 6 dependentsmodeloriented
modelStudio:Interactive Studio for Explanatory Model Analysis
Automate the explanatory analysis of machine learning predictive models. Generate advanced interactive model explanations in the form of a serverless HTML site with only one line of code. This tool is model-agnostic, therefore compatible with most of the black-box predictive models and frameworks. The main function computes various (instance and model-level) explanations and produces a customisable dashboard, which consists of multiple panels for plots with their short descriptions. It is possible to easily save the dashboard and share it with others. 'modelStudio' facilitates the process of Interactive Explanatory Model Analysis introduced in Baniecki et al. (2023) <doi:10.1007/s10618-023-00924-w>.
Maintained by Hubert Baniecki. Last updated 2 years ago.
aiexplainableexplainable-aiexplainable-machine-learningexplanatory-model-analysishumanimlinteractiveinteractivityinterpretabilityinterpretableinterpretable-machine-learninglearningmachinemodelmodel-visualizationvisualizationxai
331 stars 7.92 score 56 scriptsbioc
scDD:Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.
Maintained by Keegan Korthauer. Last updated 5 months ago.
immunooncologybayesianclusteringrnaseqsinglecellmultiplecomparisonvisualizationdifferentialexpression
33 stars 7.92 score 50 scripts
cpanse
protViz:Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
Maintained by Christian Panse. Last updated 1 years ago.
funmass-spectrometrypeptide-identificationproteomicsquantificationvisualizationcpp
11 stars 7.88 score 72 scripts 2 dependentsbioc
ChemmineOB:R interface to a subset of OpenBabel functionalities
ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.
Maintained by Thomas Girke. Last updated 5 months ago.
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicsopenbabelcpp
10 stars 7.87 score 77 scripts 1 dependentsbioc
fishpond:Fishpond: downstream methods and tools for expression data
Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files.
Maintained by Michael Love. Last updated 5 months ago.
sequencingrnaseqgeneexpressiontranscriptionnormalizationregressionmultiplecomparisonbatcheffectvisualizationdifferentialexpressiondifferentialsplicingalternativesplicingsinglecellbioconductorgene-expressiongenomicssalmonscrnaseqstatisticstranscriptomics
28 stars 7.83 score 150 scripts
teunbrand
legendry:Extended Legends and Axes for 'ggplot2'
A 'ggplot2' extension that focusses on expanding the plotter's arsenal of guides. Guides in 'ggplot2' include axes and legends. 'legendry' offers new axes and annotation options, as well as new legends and colour displays.
Maintained by Teun van den Brand. Last updated 23 days ago.
axisaxis-customizationggplot-extensionggplot2legendvisualization
227 stars 7.83 score 29 scripts 2 dependents
relund
gMOIP:Tools for 2D and 3D Plots of Single and Multi-Objective Linear/Integer Programming Models
Make 2D and 3D plots of linear programming (LP), integer linear programming (ILP), or mixed integer linear programming (MILP) models with up to three objectives. Plots of both the solution and criterion space are possible. For instance the non-dominated (Pareto) set for bi-objective LP/ILP/MILP programming models (see vignettes for an overview). The package also contains an function for checking if a point is inside the convex hull.
Maintained by Lars Relund Nielsen. Last updated 5 months ago.
2d-plot3d-plotbi-objectiveconvex-hullinteger-programminglinear-programmingmathmilpmixed-integer-programmingmulti-objectivepolytopetri-objectivevisualization
5 stars 7.81 score 79 scripts 3 dependentsbioc
PhyloProfile:PhyloProfile
PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.
Maintained by Vinh Tran. Last updated 7 days ago.
softwarevisualizationdatarepresentationmultiplecomparisonfunctionalpredictiondimensionreductionbioinformaticsheatmapinteractive-visualizationsorthologsphylogenetic-profileshiny
33 stars 7.79 score 10 scripts
alastairrushworth
inspectdf:Inspection, Comparison and Visualisation of Data Frames
A collection of utilities for columnwise summary, comparison and visualisation of data frames. Functions report missingness, categorical levels, numeric distribution, correlation, column types and memory usage.
Maintained by Alastair Rushworth. Last updated 3 years ago.
comparisondataframeedaexploratory-data-analysisvisualizationcpp
251 stars 7.77 score 444 scripts 1 dependentsbioc
KEGGgraph:KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.
Maintained by Jitao David Zhang. Last updated 5 months ago.
pathwaysgraphandnetworkvisualizationkegg
7.76 score 114 scripts 23 dependentsbioc
DEXSeq:Inference of differential exon usage in RNA-Seq
The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
Maintained by Alejandro Reyes. Last updated 28 days ago.
immunooncologysequencingrnaseqdifferentialexpressionalternativesplicingdifferentialsplicinggeneexpressionvisualization
7.75 score 330 scripts 6 dependentsbioc
coRdon:Codon Usage Analysis and Prediction of Gene Expressivity
Tool for analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences. Calculates different measures of CU bias and CU-based predictors of gene expressivity, and performs gene set enrichment analysis for annotated sequences. Implements several methods for visualization of CU and enrichment analysis results.
Maintained by Anamaria Elek. Last updated 5 months ago.
softwaremetagenomicsgeneexpressiongenesetenrichmentgenepredictionvisualizationkeggpathwaysgenetics cellbiologybiomedicalinformaticsimmunooncology
20 stars 7.71 score 48 scripts 1 dependentsbioc
FlowSOM:Using self-organizing maps for visualization and interpretation of cytometry data
FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.
Maintained by Sofie Van Gassen. Last updated 5 months ago.
cellbiologyflowcytometryclusteringvisualizationsoftwarecellbasedassays
7.71 score 468 scripts 10 dependentsbioc
countsimQC:Compare Characteristic Features of Count Data Sets
countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.
Maintained by Charlotte Soneson. Last updated 3 months ago.
microbiomernaseqsinglecellexperimentaldesignqualitycontrolreportwritingvisualizationimmunooncology
27 stars 7.69 score 24 scriptsbioc
phantasus:Visual and interactive gene expression analysis
Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus โ a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.
Maintained by Alexey Sergushichev. Last updated 5 months ago.
geneexpressionguivisualizationdatarepresentationtranscriptomicsrnaseqmicroarraynormalizationclusteringdifferentialexpressionprincipalcomponentimmunooncology
43 stars 7.68 score 15 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
Mfuzz:Soft clustering of omics time series data
The Mfuzz package implements noise-robust soft clustering of omics time-series data, including transcriptomic, proteomic or metabolomic data. It is based on the use of c-means clustering. For convenience, it includes a graphical user interface.
Maintained by Matthias Futschik. Last updated 5 months ago.
microarrayclusteringtimecoursepreprocessingvisualization
7.64 score 338 scripts 4 dependentsbioc
Heatplus:Heatmaps with row and/or column covariates and colored clusters
Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.
Maintained by Alexander Ploner. Last updated 5 months ago.
7.63 score 94 scripts 5 dependents
dominikrafacz
deepdep:Visualise and Explore the Deep Dependencies of R Packages
Provides tools for exploration of R package dependencies. The main deepdep() function allows to acquire deep dependencies of any package and plot them in an elegant way. It also adds some popularity measures for the packages e.g. in the form of download count through the 'cranlogs' package. Uses the CRAN metadata database <http://crandb.r-pkg.org> and Bioconductor metadata <http://bioconductor.org>. Other data acquire functions are: get_dependencies(), get_downloads() and get_description(). The deepdep_shiny() function runs shiny application that helps to produce a nice 'deepdep' plot.
Maintained by Dominik Rafacz. Last updated 2 years ago.
74 stars 7.60 score 90 scriptshrbrmstr
vegalite:Tools to Encode Visualizations with the 'Grammar of Graphics'-Like 'Vega-Lite' 'Spec'
The 'Vega-Lite' 'JavaScript' framework provides a higher-level grammar for visual analysis, akin to 'ggplot' or 'Tableau', that generates complete 'Vega' specifications. Functions exist which enable building a valid 'spec' from scratch or importing a previously created 'spec' file. Functions also exist to export 'spec' files and to generate code which will enable plots to be embedded in properly configured web pages. The default behavior is to generate an 'htmlwidget'.
Maintained by Bob Rudis. Last updated 7 years ago.
data-visualizationdatavisualizationvega-litevega-lite-specvisualizationwidget
158 stars 7.60 score 84 scripts
flr
ggplotFL:Using ggplot2 in FLR
Using ggplot2 for FLR. Provides (1) overloaded ggplot methods for various FLR classes, (2) ggplot-based versions of standard plots in the FLCore package, and (3) new geoms for using FLR objects.
Maintained by Iago Mosqueira. Last updated 2 months ago.
visualizationggplot2fisheriesflr
4 stars 7.60 score 458 scripts 12 dependents
tidymodels
modeldb:Fits Models Inside the Database
Uses 'dplyr' and 'tidyeval' to fit statistical models inside the database. It currently supports KMeans and linear regression models.
Maintained by Max Kuhn. Last updated 1 years ago.
databasedbplyrdplyrggplot2modelingrlangsqltidyevalvisualization
79 stars 7.59 score 62 scriptsbioc
AlpsNMR:Automated spectraL Processing System for NMR
Reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra proccessing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available.
Maintained by Sergio Oller Moreno. Last updated 5 months ago.
softwarepreprocessingvisualizationclassificationcheminformaticsmetabolomicsdataimport
15 stars 7.59 score 12 scripts 1 dependentsbioc
ggsc:Visualizing Single Cell and Spatial Transcriptomics
Useful functions to visualize single cell and spatial data. It supports visualizing 'Seurat', 'SingleCellExperiment' and 'SpatialExperiment' objects through grammar of graphics syntax implemented in 'ggplot2'.
Maintained by Guangchuang Yu. Last updated 5 months ago.
dimensionreductiongeneexpressionsinglecellsoftwarespatialtranscriptomicsvisualizationopenblascppopenmp
47 stars 7.59 score 18 scriptsbioc
TSCAN:Tools for Single-Cell Analysis
Provides methods to perform trajectory analysis based on a minimum spanning tree constructed from cluster centroids. Computes pseudotemporal cell orderings by mapping cells in each cluster (or new cells) to the closest edge in the tree. Uses linear modelling to identify differentially expressed genes along each path through the tree. Several plotting and interactive visualization functions are also implemented.
Maintained by Zhicheng Ji. Last updated 5 months ago.
geneexpressionvisualizationgui
7.58 score 207 scripts 3 dependentsbioc
dittoSeq:User Friendly Single-Cell and Bulk RNA Sequencing Visualization
A universal, user friendly, single-cell and bulk RNA sequencing visualization toolkit that allows highly customizable creation of color blindness friendly, publication-quality figures. dittoSeq accepts both SingleCellExperiment (SCE) and Seurat objects, as well as the import and usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data. Visualizations include dimensionality reduction plots, heatmaps, scatterplots, percent composition or expression across groups, and more. Customizations range from size and title adjustments to automatic generation of annotations for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton plot, hidden data overlay upon cursor hovering via ggplotly conversion, and many more. All with simple, discrete inputs. Color blindness friendliness is powered by legend adjustments (enlarged keys), and by allowing the use of shapes or letter-overlay in addition to the carefully selected dittoColors().
Maintained by Daniel Bunis. Last updated 5 months ago.
softwarevisualizationrnaseqsinglecellgeneexpressiontranscriptomicsdataimport
7.56 score 760 scripts 2 dependents
alextkalinka
linkcomm:Tools for Generating, Visualizing, and Analysing Link Communities in Networks
Link communities reveal the nested and overlapping structure in networks, and uncover the key nodes that form connections to multiple communities. linkcomm provides a set of tools for generating, visualizing, and analysing link communities in networks of arbitrary size and type. The linkcomm package also includes tools for generating, visualizing, and analysing Overlapping Cluster Generator (OCG) communities. Kalinka and Tomancak (2011) <doi:10.1093/bioinformatics/btr311>.
Maintained by Alex T. Kalinka. Last updated 4 years ago.
clusteringnetworksnetworks-biologyvisualizationcpp
7 stars 7.53 score 115 scripts 4 dependents
tongzhou2017
itol.toolkit:Helper Functions for 'Interactive Tree Of Life'
The 'Interactive Tree Of Life' <https://itol.embl.de/> online server can edit and annotate trees interactively. The 'itol.toolkit' package can support all types of annotation templates.
Maintained by Tong Zhou. Last updated 4 months ago.
bioinformaticsitolvisualization
167 stars 7.48 score 60 scripts
mw201608
SuperExactTest:Exact Test and Visualization of Multi-Set Intersections
Identification of sets of objects with shared features is a common operation in all disciplines. Analysis of intersections among multiple sets is fundamental for in-depth understanding of their complex relationships. This package implements a theoretical framework for efficient computation of statistical distributions of multi-set intersections based upon combinatorial theory, and provides multiple scalable techniques for visualizing the intersection statistics. The statistical algorithm behind this package was published in Wang et al. (2015) <doi:10.1038/srep16923>.
Maintained by Minghui Wang. Last updated 1 years ago.
intersectionsetstatisticsvisualization
28 stars 7.47 score 70 scripts 1 dependentsbioc
CAGEfightR:Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.
Maintained by Malte Thodberg. Last updated 5 months ago.
softwaretranscriptioncoveragegeneexpressiongeneregulationpeakdetectiondataimportdatarepresentationtranscriptomicssequencingannotationgenomebrowsersnormalizationpreprocessingvisualization
8 stars 7.46 score 67 scripts 1 dependentsbioc
lipidr:Data Mining and Analysis of Lipidomics Datasets
lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, total chain length and unsaturation.
Maintained by Ahmed Mohamed. Last updated 5 months ago.
lipidomicsmassspectrometrynormalizationqualitycontrolvisualizationbioconductor
30 stars 7.46 score 40 scriptsbioc
HilbertCurve:Making 2D Hilbert Curve
Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the locality. This package aims to provide an easy and flexible way to visualize data through Hilbert curve.
Maintained by Zuguang Gu. Last updated 5 months ago.
softwarevisualizationsequencingcoveragegenomeannotationcpp
42 stars 7.45 score 48 scripts
jolars
qualpalr:Automatic Generation of Qualitative Color Palettes
Automatic generation of maximally distinct qualitative color palettes, optionally tailored to color deficiency. A list of colors or a subspace of a color space is used as input and then projected to the DIN99d color space, where colors that are maximally distinct are chosen algorithmically.
Maintained by Johan Larsson. Last updated 6 months ago.
23 stars 7.45 score 162 scripts 1 dependentsbioc
flowViz:Visualization for flow cytometry
Provides visualization tools for flow cytometry data.
Maintained by Mike Jiang. Last updated 5 months ago.
immunooncologyinfrastructureflowcytometrycellbasedassaysvisualization
7.44 score 231 scripts 12 dependentsbioc
GenomicDistributions:GenomicDistributions: fast analysis of genomic intervals with Bioconductor
If you have a set of genomic ranges, this package can help you with visualization and comparison. It produces several kinds of plots, for example: Chromosome distribution plots, which visualize how your regions are distributed over chromosomes; feature distance distribution plots, which visualizes how your regions are distributed relative to a feature of interest, like Transcription Start Sites (TSSs); genomic partition plots, which visualize how your regions overlap given genomic features such as promoters, introns, exons, or intergenic regions. It also makes it easy to compare one set of ranges to another.
Maintained by Kristyna Kupkova. Last updated 5 months ago.
softwaregenomeannotationgenomeassemblydatarepresentationsequencingcoveragefunctionalgenomicsvisualization
26 stars 7.44 score 25 scriptsbioc
HPAanalyze:Retrieve and analyze data from the Human Protein Atlas
Provide functions for retrieving, exploratory analyzing and visualizing the Human Protein Atlas data.
Maintained by Anh Nhat Tran. Last updated 5 months ago.
proteomicscellbiologyvisualizationsoftware
35 stars 7.43 score 37 scripts
amices
ggmice:Visualizations for 'mice' with 'ggplot2'
Enhance a 'mice' imputation workflow with visualizations for incomplete and/or imputed data. The plotting functions produce 'ggplot' objects which may be easily manipulated or extended. Use 'ggmice' to inspect missing data, develop imputation models, evaluate algorithmic convergence, or compare observed versus imputed data.
Maintained by Hanne Oberman. Last updated 8 months ago.
32 stars 7.42 score 165 scripts
xd-deng
ECharts2Shiny:Embedding Interactive Charts Generated with ECharts Library into Shiny Applications
Embed interactive charts to their Shiny applications. These charts will be generated by ECharts library developed by Baidu (<http://echarts.baidu.com/>). Current version supports line chart, bar chart, pie chart, scatter plot, gauge, word cloud, radar chart, tree map, and heat map.
Maintained by Xiaodong Deng. Last updated 4 years ago.
129 stars 7.42 score 135 scriptsbioc
genefu:Computation of Gene Expression-Based Signatures in Breast Cancer
This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.
Maintained by Benjamin Haibe-Kains. Last updated 4 months ago.
differentialexpressiongeneexpressionvisualizationclusteringclassification
7.42 score 193 scripts 3 dependents
nsgrantham
ggdark:Dark Mode for 'ggplot2' Themes
Activate dark mode on your favorite 'ggplot2' theme with dark_mode() or use the dark versions of 'ggplot2' themes, including dark_theme_gray(), dark_theme_minimal(), and others. When a dark theme is applied, all geom color and geom fill defaults are changed to make them visible against a dark background. To restore the defaults to their original values, use invert_geom_defaults().
Maintained by Neal Grantham. Last updated 6 years ago.
darkmodeggplot2ggplot2-themestidyversevisualization
200 stars 7.37 score 788 scripts 1 dependentsbioc
cogena:co-expressed gene-set enrichment analysis
cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.
Maintained by Zhilong Jia. Last updated 5 months ago.
clusteringgenesetenrichmentgeneexpressionvisualizationpathwayskegggomicroarraysequencingsystemsbiologydatarepresentationdataimportbioconductorbioinformatics
12 stars 7.36 score 32 scripts
eltebioinformatics
mulea:Enrichment Analysis Using Multiple Ontologies and False Discovery Rate
Background - Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. Results - mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. Conclusions - mulea is distributed as a CRAN R package. It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.
Maintained by Tamas Stirling. Last updated 4 months ago.
annotationdifferentialexpressiongeneexpressiongenesetenrichmentgographandnetworkmultiplecomparisonpathwaysreactomesoftwaretranscriptionvisualizationenrichmentenrichment-analysisfunctional-enrichment-analysisgene-set-enrichmentontologiestranscriptomicscpp
28 stars 7.36 score 34 scripts
kanaries
GWalkR:Interactive Exploratory Data Analysis Tool
Simplify your R data analysis and data visualization workflow by turning your data frame into an interactive 'Tableau'-like interface, leveraging the 'graphic-walker' JavaScript library and the 'htmlwidgets' package.
Maintained by Yue Yu. Last updated 19 hours ago.
data-visualizationggplot2tableau-alternativevisualization
462 stars 7.31 score 45 scriptsbioc
NormalyzerDE:Evaluation of normalization methods and calculation of differential expression analysis statistics
NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices using both existing approaches and a novel time-segmented approach, calculates performance measures and generates an evaluation report. Furthermore, it provides an easy utility for Limma- or ANOVA- based differential expression analysis.
Maintained by Jakob Willforss. Last updated 5 months ago.
normalizationmultiplecomparisonvisualizationbayesianproteomicsmetabolomicsdifferentialexpressionbioconductorbioinformaticslimma
22 stars 7.30 score 38 scripts 1 dependentsbioc
flowClust:Clustering for Flow Cytometry
Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'.
Maintained by Greg Finak. Last updated 5 months ago.
immunooncologyclusteringvisualizationflowcytometry
7.30 score 83 scripts 6 dependentsbioc
regionReport:Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder. You can also create reports for DESeq2 or edgeR results.
Maintained by Leonardo Collado-Torres. Last updated 2 months ago.
differentialexpressionsequencingrnaseqsoftwarevisualizationtranscriptioncoveragereportwritingdifferentialmethylationdifferentialpeakcallingimmunooncologyqualitycontrolbioconductorderfinderdeseq2edgerregionreportrmarkdown
9 stars 7.22 score 46 scripts
hneth
riskyr:Rendering Risk Literacy more Transparent
Risk-related information (like the prevalence of conditions, the sensitivity and specificity of diagnostic tests, or the effectiveness of interventions or treatments) can be expressed in terms of frequencies or probabilities. By providing a toolbox of corresponding metrics and representations, 'riskyr' computes, translates, and visualizes risk-related information in a variety of ways. Adopting multiple complementary perspectives provides insights into the interplay between key parameters and renders teaching and training programs on risk literacy more transparent.
Maintained by Hansjoerg Neth. Last updated 10 months ago.
2x2-matrixbayesian-inferencecontingency-tablerepresentationriskrisk-literacyvisualization
19 stars 7.18 score 80 scriptsbioc
TnT:Interactive Visualization for Genomic Features
A R interface to the TnT javascript library (https://github.com/ tntvis) to provide interactive and flexible visualization of track-based genomic data.
Maintained by Jialin Ma. Last updated 5 months ago.
infrastructurevisualizationbioconductorgenome-browserhtmlwidgetsshiny
14 stars 7.15 score 17 scriptsbioc
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 dependents
egenn
rtemis:Machine Learning and Visualization
Advanced Machine Learning and Visualization. Unsupervised Learning (Clustering, Decomposition), Supervised Learning (Classification, Regression), Cross-Decomposition, Bagging, Boosting, Meta-models. Static and interactive graphics.
Maintained by E.D. Gennatas. Last updated 2 months ago.
data-sciencedata-visualizationmachine-learningmachine-learning-libraryvisualization
145 stars 7.09 score 50 scripts 2 dependentscbailiss
basictabler:Construct Rich Tables for Output to 'HTML'/'Excel'
Easily create tables from data frames/matrices. Create/manipulate tables row-by-row, column-by-column or cell-by-cell. Use common formatting/styling to output rich tables as 'HTML', 'HTML widgets' or to 'Excel'.
Maintained by Christopher Bailiss. Last updated 4 years ago.
htmlhtmlwidgettablesvisualization
37 stars 7.09 score 94 scripts
smin95
smplot2:Create Standalone and Composite Plots in 'ggplot2' for Publications
Provides functions for creating and annotating a composite plot in 'ggplot2'. Offers background themes and shortcut plotting functions that produce figures that are appropriate for the format of scientific journals. Some methods are described in Min and Zhou (2021) <doi:10.3389/fgene.2021.802894>.
Maintained by Seung Hyun Min. Last updated 2 months ago.
easy-to-useggplot2scientific-visualizationvisualization
24 stars 7.08 score 288 scripts 1 dependentsguangchuangyu
meme:Create Meme
The word 'Meme' was originated from the book, 'The Selfish Gene', authored by Richard Dawkins (1976). It is a unit of culture that is passed from one generation to another and correlates to the gene, the unit of physical heredity. The internet memes are captioned photos that are intended to be funny, ridiculous. Memes behave like infectious viruses and travel from person to person quickly through social media. The 'meme' package allows users to make custom memes.
Maintained by Guangchuang Yu. Last updated 4 years ago.
45 stars 7.08 score 54 scripts
rchlumsk
RavenR:Raven Hydrological Modelling Framework R Support and Analysis
Utilities for processing input and output files associated with the Raven Hydrological Modelling Framework. Includes various plotting functions, model diagnostics, reading output files into extensible time series format, and support for writing Raven input files. The 'RavenR' package is also archived at Chlumsky et al. (2020) <doi:10.5281/zenodo.4248183>. The Raven Hydrologic Modelling Framework method can be referenced with Craig et al. (2020) <doi:10.1016/j.envsoft.2020.104728>.
Maintained by Robert Chlumsky. Last updated 5 months ago.
diagnosticshydrologymodelingmodellingvisualizationwaterwater-resourceswatershedcpp
36 stars 7.06 score 20 scriptsbioc
cardelino:Clone Identification from Single Cell Data
Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.
Maintained by Davis McCarthy. Last updated 5 months ago.
singlecellrnaseqvisualizationtranscriptomicsgeneexpressionsequencingsoftwareexomeseqclonal-clusteringgibbs-samplingscrna-seqsingle-cellsomatic-mutations
61 stars 7.05 score 62 scriptsbioc
fmcsR:Mismatch Tolerant Maximum Common Substructure Searching
The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.
Maintained by Thomas Girke. Last updated 5 months ago.
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp
5 stars 7.03 score 60 scripts 1 dependentsbioc
ACE:Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
Uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers.
Maintained by Jos B Poell. Last updated 5 months ago.
copynumbervariationdnaseqcoveragewholegenomevisualizationsequencing
15 stars 7.03 score 18 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 dependentserocoar
ggpol:Visualizing Social Science Data with 'ggplot2'
A 'ggplot2' extension for implementing parliament charts and several other useful visualizations.
Maintained by Frederik Tiedemann. Last updated 3 years ago.
datavizggplot-extensionggplot2visualization
104 stars 7.00 score 212 scripts 1 dependentsbioc
satuRn:Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
satuRn provides a higly performant and scalable framework for performing differential transcript usage analyses. The package consists of three main functions. The first function, fitDTU, fits quasi-binomial generalized linear models that model transcript usage in different groups of interest. The second function, testDTU, tests for differential usage of transcripts between groups of interest. Finally, plotDTU visualizes the usage profiles of transcripts in groups of interest.
Maintained by Jeroen Gilis. Last updated 5 months ago.
regressionexperimentaldesigndifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization
21 stars 6.97 score 74 scripts 1 dependentsbioc
NanoMethViz:Visualise methylation data from Oxford Nanopore sequencing
NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.
Maintained by Shian Su. Last updated 19 days ago.
softwarelongreadvisualizationdifferentialmethylationdnamethylationepigeneticsdataimportzlibcpp
26 stars 6.95 score 11 scriptsbioc
psichomics:Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.
Maintained by Nuno Saraiva-Agostinho. Last updated 5 months ago.
sequencingrnaseqalternativesplicingdifferentialsplicingtranscriptionguiprincipalcomponentsurvivalbiomedicalinformaticstranscriptomicsimmunooncologyvisualizationmultiplecomparisongeneexpressiondifferentialexpressionalternative-splicingbioconductordata-analysesdifferential-gene-expressiondifferential-splicing-analysisgene-expressiongtexrecount2rna-seq-datasplicing-quantificationsratcgavast-toolscpp
36 stars 6.95 score 31 scriptsbioc
animalcules:Interactive microbiome analysis toolkit
animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.
Maintained by Jessica McClintock. Last updated 5 months ago.
microbiomemetagenomicscoveragevisualization
55 stars 6.95 score 23 scripts
vegawidget
altair:Interface to 'Altair'
Interface to 'Altair' <https://altair-viz.github.io>, which itself is a 'Python' interface to 'Vega-Lite' <https://vega.github.io/vega-lite/>. This package uses the 'Reticulate' framework <https://rstudio.github.io/reticulate/> to manage the interface between R and 'Python'.
Maintained by Ian Lyttle. Last updated 1 years ago.
altairinteractivereticulatevega-litevisualization
91 stars 6.94 score 23 scripts 1 dependentsbioc
RCM:Fit row-column association models with the negative binomial distribution for the microbiome
Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.
Maintained by Stijn Hawinkel. Last updated 5 months ago.
metagenomicsdimensionreductionmicrobiomevisualizationordinationphyloseqrcm
16 stars 6.90 score 25 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 scripts