clusterProfiler - A Universal Enrichment Tool for Interpreting Omics Data
A universal tool for interpreting functional characteristics of omics data. It supports Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA) for both coding and non-coding genomics data of thousands of species. It provides a unified and tidy interface to access, manipulate, and visualize enrichment results. A key capability is the simultaneous analysis and comparison of datasets from multiple treatments or time points. It also provides high-level access to topology-aware enrichment workflows powered by 'enrichit', including single-network and multi-layer network enrichment for Gene Ontology and KEGG analyses. Furthermore, it integrates Large Language Model (LLM) capabilities to provide automated and insightful interpretation of enrichment results.
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annotationclusteringgenesetenrichmentgokeggmultiplecomparisonpathwaysreactomevisualizationenrichment-analysisgseaquarto
18.06 score 1.2k stars 63 dependents 25k scripts 62k downloadsggtree - 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.
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alignmentannotationclusteringdataimportmultiplesequencealignmentphylogeneticsreproducibleresearchsoftwarevisualizationannotationsggplot2phylogenetic-trees
17.66 score 935 stars 129 dependents 9.9k scripts 74k downloadsenrichplot - Visualization of Functional Enrichment Result
The 'enrichplot' package provides visualization methods for interpreting functional enrichment results from ORA or GSEA analyses. It is designed to work with the 'clusterProfiler' ecosystem and builds on 'ggplot2' for flexible and extensible graphics.
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annotationgenesetenrichmentgokeggpathwayssoftwarevisualizationenrichment-analysispathway-analysis
16.79 score 259 stars 74 dependents 7.4k scripts 67k downloadsDOSE - Disease Ontology Semantic and Enrichment analysis
Provides ontology-aware methods for disease and phenotype knowledge mining. DOSE supports semantic similarity analysis of disease and phenotype ontology terms, genes, and gene clusters using methods including Resnik, Schlicker, Jiang, Lin, and Wang. It also provides over-representation analysis and gene set enrichment analysis for interpreting gene vectors and ranked gene lists in disease, phenotype, and cancer contexts.
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annotationvisualizationmultiplecomparisongenesetenrichmentpathwayssoftwaredisease-ontologyenrichment-analysissemantic-similarityquarto
15.66 score 125 stars 75 dependents 3.1k scripts 53k downloadsGOSemSim - GO-terms Semantic Similarity Measures
Semantic similarity analysis of Gene Ontology (GO) annotations provides a quantitative framework for comparing GO terms, gene products, and gene clusters. GOSemSim implements widely used information content- and graph-based similarity measures, including the methods of Resnik, Schlicker, Jiang, Lin, Wang and TCSS. It also provides utilities for preparing annotation data and combining term-level similarities into gene- and cluster-level scores.
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annotationgoclusteringpathwaysnetworksoftwarebioinformaticsgene-ontologysemantic-similarityquartocpp
14.85 score 75 stars 85 dependents 962 scripts 47k downloadsChIPseeker - 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.
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annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics
13.95 score 259 stars 7 dependents 3.5k scripts 5.8k downloadsggplotify - Convert Plot to 'grob' or 'ggplot' Object
Convert plot function call (using expression or formula) to 'grob' or 'ggplot' object that compatible to the 'grid' and 'ggplot2' ecosystem. With this package, we are able to e.g. using 'cowplot' to align plots produced by 'base' graphics, 'ComplexHeatmap', 'eulerr', 'grid', 'lattice', 'magick', 'pheatmap', 'vcd' etc. by converting them to 'ggplot' objects.
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baseplotggplot2gridlatticeupsetrvcd
13.76 score 115 stars 201 dependents 3.3k scripts 72k downloadsscatterpie - Scatter Pie Plot
Creates scatterpie plots, especially useful for plotting pies on a map.
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13.42 score 67 stars 87 dependents 1.3k scripts 41k downloadsReactomePA - Reactome Pathway Analysis
This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis, network-based enrichment analysis (NSEA) on the Reactome reaction graph, Bayesian term selection, weighted enrichment, and several functions for visualization. This package is not affiliated with the Reactome team.
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pathwaysvisualizationannotationmultiplecomparisongenesetenrichmentreactomeenrichment-analysisreactome-pathway-analysisreactomepa
13.14 score 46 stars 12 dependents 2.5k scripts 9.7k downloadsggimage - Use Images in 'ggplot2'
Add image layers to 'ggplot2' plots. Images can be placed at data coordinates, used as plot backgrounds, or embedded as subplots. Supports local image files, image URLs, and image sources including 'PhyloPic', 'Pokemon', emoji, and icons. Interactive image layers are available for 'HTML' output.
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ggplot2imagevisualizationquarto
12.93 score 179 stars 14 dependents 3.9k scripts 7.3k downloadsaplot - Decorate a 'ggplot' with Associated Information
Supports data-driven composition of a main plot with associated subplots that need precise axis alignment. Unlike general layout-focused tools such as 'cowplot' and 'patchwork', it enables related subplots to be integrated on the top, bottom, left, or right sides of a main plot with matched axes, so that the combined panels can be interpreted as a coherent whole. This design was inspired by the 'Method 2' described in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>).
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12.58 score 131 stars 143 dependents 1.0k scripts 87k downloadshexSticker - Create Hexagon Sticker in R
Helper functions for creating reproducible hexagon sticker purely in R.
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ggplot2hexagon-stickerlogostickersvisualization
11.66 score 813 stars 2 dependents 2.6k scripts 1.4k downloadsggfun - Miscellaneous Functions for 'ggplot2'
Provides a collection of 'ggplot2' extensions and utilities for creating geometric layers, applying themes, working with legends, and modifying plot objects.
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11.30 score 18 stars 176 dependents 147 scripts 71k downloadstidytree - A Tidy Tool for Phylogenetic Tree Data Manipulation
Phylogenetic trees contain components such as nodes, edges, branches, and associated data. As the core data manipulation tool in the 'ggtree' ecosystem, 'tidytree' provides tools for converting tree objects to tidy data frames and tidy interfaces for manipulating, analyzing, and visualizing tree data.
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phylogenetic-treetidyversetree-data
11.25 score 61 stars 156 dependents 70k downloadsggbreak - Set Axis Break for 'ggplot2'
An implementation of scale functions for setting axis breaks of a 'gg' plot (S Xu (2021) <doi:10.3389/fgene.2021.774846>).
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axis-breakcut-plotggbreakggplot2wrap-plot
11.18 score 148 stars 2 dependents 2.5k scripts 8.4k downloadstidydr - Unify Dimensionality Reduction Results
Dimensionality reduction is widely used in many domains for analyzing and visualizing high-dimensional data. 'tidydr' provides uniform output and is compatible with multiple methods, including 'prcomp', 'cmdscale', 'Rtsne', 'umap' and 'metaMDS'. Any function returning a numeric matrix can also be used. The unified result can be visualized directly with 'ggplot2', and several methods can be run and compared in a single call.
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10.76 score 15 stars 76 dependents 237 scripts 24k downloadsshadowtext - Shadow Text Grob and Layer
Implement shadowtextGrob() for 'grid' and geom_shadowtext() layer for 'ggplot2'. These functions create/draw text grob with background shadow.
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10.69 score 41 stars 12 dependents 712 scripts 23k downloadsscholar - Analyse Citation Data from Google Scholar
Provides tools to retrieve, analyse, and format publication and citation data from Google Scholar profiles. It supports profile lookup, publication records, citation histories, scholar comparison, coauthor networks, journal ranking queries, CV-ready publication lists, and citation metric summaries.
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10.49 score 53 stars 2 dependents 547 scripts 2.5k downloads
treeio - Base Classes and Functions for Phylogenetic Tree Input and Output
'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.
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softwareannotationclusteringdataimportdatarepresentationalignmentmultiplesequencealignmentphylogeneticsexporterparserphylogenetic-trees
10.07 score 105 stars 144 dependents 4 scripts
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.
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softwarevisualizationalignmentannotationmultiplesequencealignment
9.81 score 220 stars 1 dependents 296 scripts 1.2k downloadsyulab.utils - Supporting Functions for Packages Maintained by 'YuLab-SMU'
Miscellaneous functions commonly used by 'YuLab-SMU'.
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9.78 score 38 stars 271 dependents 94k downloadsemojifont - Emoji and Font Awesome in Graphics
An implementation of using emoji and fontawesome for using in both base and 'ggplot2' graphics.
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emojifont-awesomeggplot2visualizationquarto
8.76 score 67 stars 3 dependents 1.5k scripts 1.3k downloadsgson - Base Class and Methods for 'gson' Format
Provides a lightweight container and exchange format for gene set collections. A 'GSON' object stores which genes belong to which gene set, together with gene set and gene names, the identifier types in use, species, versions and source metadata. A collection can be built from data frames, read from and written to the 'gson' JavaScript Object Notation (JSON) format and the 'GMT' format, subset by gene set, merged across sources, validated, and resolved to the web addresses of the databases it comes from, so that a collection gathered by one package can be analysed by another.
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8.75 score 3 stars 82 dependents 80 scripts 48k downloadsbadger - Badge for R Package
Query information and generate badge for using in README and GitHub Pages.
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badge
8.64 score 210 stars 5 dependents 236 scripts 1.1k downloadsggtangle - Draw Network with Data
Extends the 'ggplot2' plotting system to support network visualization. Inspired by the 'Method 1' in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>), 'ggtangle' is designed to work with network associated data.
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7.91 score 1 stars 76 dependents 27 scripts 37k downloadsdlstats - Download Stats of R Packages
Monthly download stats of 'CRAN' and 'Bioconductor' packages. Download stats of 'CRAN' packages is from the 'RStudio' 'CRAN mirror', see <https://cranlogs.r-pkg.org:443>. 'Bioconductor' package download stats is at <https://bioconductor.org/packages/stats/>.
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7.75 score 14 stars 7 dependents 64 scripts 1.2k downloadsggsc - 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'.
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dimensionreductiongeneexpressionsinglecellsoftwarespatialtranscriptomicsvisualizationopenblascppopenmp
7.52 score 51 stars 37 scripts 346 downloadsMicrobiomeProfiler - An R/shiny package for microbiome functional enrichment analysis
This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.
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microbiomesoftwarevisualizationkegg
7.49 score 42 stars 42 scripts 444 downloadsmeme - 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.
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gridmemevisualization
7.23 score 48 stars 70 scripts 574 downloadsmeshes - MeSH Enrichment and Semantic analyses
Provides tools for MeSH (Medical Subject Headings) enrichment and semantic similarity analysis. The package uses MeSH term annotations linked to Entrez Gene identifiers through gendoo, gene2pubmed and RBBH, enabling over-representation analysis, gene set enrichment analysis and semantic comparison of gene lists or ranked expression profiles. It implements Resnik, Schlicker, Jiang, Lin and Wang similarity methods for comparing MeSH terms, genes and gene groups across more than 70 species.
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annotationclusteringmultiplecomparisonsoftwareenrichment-analysismedical-subject-headingssemantic-similarityquarto
6.83 score 13 stars 584 downloadsrvcheck - R/Package Version Check
Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').
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6.65 score 23 stars 7 dependents 50 scripts 1.9k downloadsseqcombo - Visualization Tool for Genetic Reassortment
Provides useful functions for visualizing virus reassortment events.
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alignmentsoftwarevisualization
5.92 score 21 stars 7 scripts 392 downloadsepiSeeker - epiSeeker: an R package for Annotation, Comparison and Visualization of multi-omics epigenetic data
This package implements functions to analyze multi-omics epigenetic data. Data of fragment type and base type are supported by epiSeeker. It provides functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statistical methods to estimate the significance of overlap among peak data sets, and motif analysis. It incorporates the GEO database for users to compare their own dataset with those deposited in the 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, overlap of peaks or genes, and the single-base resolution epigenetic data by considering the strand, motif, and additional information.
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annotationchipseqsoftwarevisualizationmultiplecomparisoncoveragemotifannotationgeneregulation
5.38 score 223 downloadsivolcano - Interactive Volcano Plot
Generate interactive volcano plots for exploring gene expression data. Built with 'ggplot2', the plots are rendered interactive using 'ggiraph', enabling users to hover over points to display detailed information or click to trigger custom actions.
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5.32 score 7 stars 4 scripts 421 downloadsggtreeSpace - Visualizing Phylomorphospaces using 'ggtree'
This package is a comprehensive visualization tool specifically designed for exploring phylomorphospace. It not only simplifies the process of generating phylomorphospace, but also enhances it with the capability to add graphic layers to the plot with grammar of graphics to create fully annotated phylomorphospaces. It also provide some utilities to help interpret evolutionary patterns.
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annotationvisualizationphylogeneticssoftware
5.32 score 5 stars 14 scripts 262 downloadswikiprofiler - Data Integration and Visualization on 'WikiPathways' Graphics
Retrieves pathway graphics from 'WikiPathways' and maps user-supplied quantitative data, such as gene expression values, onto pathway nodes. Provides a pipe-friendly grammar for building pathway visualizations with layered fills, text highlighting, condition-wise comparisons, data preparation helpers, and batch rendering utilities.
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5.26 score 6 stars 412 downloadsshinyTempSignal - Explore Temporal and Other Phylogenetic Signals
Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels. The method was extended to support exploring other phylogenetic signals under strict and relaxed models.
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molecular-clockphylogeneticsshiny-app
5.26 score 9 stars 321 downloadsTDbook - Companion Package for the Book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574, doi:10.1201/9781003279242)
The companion package that provides all the datasets used in the book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574, doi:10.1201/9781003279242).
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5.10 score 13 stars 97 scripts 421 downloadsaplotExtra - Creating Composite Plots using 'aplot'
Many complex plots are actually composite plots, such as 'oncoplot', 'funkyheatmap', 'upsetplot', etc. We can produce subplots using 'ggplot2' and combine them to create composite plots using 'aplot'. In this way, it is easy to customize these complex plots, by adding, deleting or modifying subplots in the final plot. This package provides a set of utilities to help users to create subplots and complex plots.
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4.48 score 10 stars 1 scripts 444 downloadsggtreeDendro - Drawing 'dendrogram' using 'ggtree'
Offers a set of 'autoplot' methods to visualize tree-like structures (e.g., hierarchical clustering and classification/regression trees) using 'ggtree'. You can adjust graphical parameters using grammar of graphic syntax and integrate external data to the tree.
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clusteringclassificationdecisiontreephylogeneticsvisualization
4.00 score 10 scripts 321 downloadswget - Setting Download Method to 'wget'
Provides function, wget_set(), to change the method (default to 'wget -c') using in download.file(). Using 'wget -c' allowing continued downloading, which is especially useful for slow internet connection and for downloading large files. User can run wget_unset() to restore previous setting.
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3.90 score 16 stars 275 downloads