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. Furthermore, it integrates Large Language Model (LLM) capabilities to provide automated and insightful interpretation of enrichment results.
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annotationclusteringgenesetenrichmentgokeggmultiplecomparisonpathwaysreactomevisualizationenrichment-analysisgseaquarto
17.35 score 1.2k stars 47 dependents 16k scripts 42k 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
17.32 score 927 stars 110 dependents 7.4k scripts 46k 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-analysisquarto
16.46 score 258 stars 56 dependents 7.1k scripts 44k downloadsDOSE - 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.
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annotationvisualizationmultiplecomparisongenesetenrichmentpathwayssoftwaredisease-ontologyenrichment-analysissemantic-similarity
15.24 score 126 stars 61 dependents 3.3k scripts 43k downloadsGOSemSim - GO-terms Semantic Similarity Measures
The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.
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annotationgoclusteringpathwaysnetworksoftwarebioinformaticsgene-ontologysemantic-similaritycpp
14.47 score 72 stars 68 dependents 840 scripts 34k 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
13.68 score 115 stars 187 dependents 3.3k scripts 65k 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
13.27 score 256 stars 4 dependents 2.7k scripts 5.1k downloadstidytree - A Tidy Tool for Phylogenetic Tree Data Manipulation
Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
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phylogenetic-treetidyversetree-data
12.91 score 60 stars 135 dependents 1.0k scripts 54k downloadsscatterpie - Scatter Pie Plot
Creates scatterpie plots, especially useful for plotting pies on a map.
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12.88 score 66 stars 69 dependents 1.3k scripts 42k downloadsaplot - Decorate a 'ggplot' with Associated Information
For many times, we are not just aligning plots as what 'cowplot' and 'patchwork' did. Users would like to align associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. Inspired by the 'Method 2' in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>), 'aplot' provides utilities to aligns associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.
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12.50 score 129 stars 121 dependents 988 scripts 55k downloadsReactomePA - 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.
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pathwaysvisualizationannotationmultiplecomparisongenesetenrichmentreactomeenrichment-analysisreactome-pathway-analysisreactomepa
12.48 score 45 stars 9 dependents 2.1k scripts 5.8k downloadsggimage - Use Image in 'ggplot2'
Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.
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ggplot2imagevisualization
12.22 score 178 stars 22 dependents 4.0k scripts 8.8k downloadshexSticker - Create Hexagon Sticker in R
Helper functions for creating reproducible hexagon sticker purely in R.
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ggplot2hexagon-stickerlogostickersvisualization
12.21 score 802 stars 12 dependents 1.9k scripts 1.4k 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
12.00 score 104 stars 126 dependents 1.9k scriptsshadowtext - 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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11.22 score 41 stars 11 dependents 872 scripts 24k 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
11.06 score 146 stars 2 dependents 2.2k scripts 10k downloadsscholar - Analyse Citation Data from Google Scholar
Provides functions to extract citation data from Google Scholar. Convenience functions are also provided for comparing multiple scholars and predicting future h-index values.
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10.89 score 51 stars 2 dependents 539 scripts 5.2k downloadsggfun - Miscellaneous Functions for 'ggplot2'
Useful functions and utilities for 'ggplot' object (e.g., geometric layers, themes, and utilities to edit the object).
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10.54 score 18 stars 162 dependents 115 scripts 57k downloadsyulab.utils - Supporting Functions for Packages Maintained by 'YuLab-SMU'
Miscellaneous functions commonly used by 'YuLab-SMU'.
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10.38 score 38 stars 256 dependents 42 scripts 81k downloads
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
9.94 score 217 stars 1 dependents 344 scripts 1.1k downloadstidydr - Unify Dimensionality Reduction Results
Dimensionality reduction (DR) is widely used in many domain for analyzing and visualizing high-dimensional data. 'tidydr' provides uniform output and is compatible with multiple methods, including 'prcomp', 'mds', 'Rtsne'. etc.
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9.77 score 15 stars 58 dependents 163 scripts 23k downloadsbadger - Badge for R Package
Query information and generate badge for using in README and GitHub Pages.
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badge
8.74 score 210 stars 5 dependents 236 scripts 1.4k 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
8.71 score 68 stars 3 dependents 1.1k scripts 1.6k 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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quarto
7.86 score 1 stars 58 dependents 27 scripts 51k 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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7.77 score 14 stars 7 dependents 74 scripts 1.4k 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
7.30 score 51 stars 37 scripts 308 downloadsmeshes - MeSH Enrichment and Semantic analyses
MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species.
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annotationclusteringmultiplecomparisonsoftwareenrichment-analysismedical-subject-headingssemantic-similarity
7.27 score 12 stars 52 scripts 569 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
7.21 score 42 stars 31 scripts 350 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
7.19 score 48 stars 64 scripts 666 downloadsenrichit - 'C++' Implementations of Functional Enrichment Analysis
Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'. Currently provides Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA). The multilevel GSEA algorithm is derived from the 'fgsea' package. Methods are described in Subramanian et al. (2005) <doi:10.1073/pnas.0506580102> and Korotkevich et al. (2021) <doi:10.1101/060012>.
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quartocpp
6.77 score 63 dependents 15 scripts 5.9k downloadsrvcheck - R/Package Version Check
Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').
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6.64 score 22 stars 7 dependents 47 scripts 2.0k downloadsseqcombo - Visualization Tool for Genetic Reassortment
Provides useful functions for visualizing virus reassortment events.
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alignmentsoftwarevisualization
5.92 score 21 stars 8 scripts 369 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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quarto
5.45 score 7 stars 6 scripts 204 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 234 downloadsgson - Base Class and Methods for 'gson' Format
Proposes a new file format ('gson') for storing gene set and related information, and provides read, write and other utilities to process this file format.
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5.32 score 53 dependents 41 scripts 32k 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 7 scripts 201 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
5.15 score 54 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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5.04 score 13 stars 85 scripts 787 downloadsseqmagick - Sequence Manipulation Utilities
Tools for reading and writing biological sequences in multiple formats, including 'FASTA', 'PHYLIP', 'CLUSTAL', 'STOCKHOLM', 'MEGA' and 'GenBank'. Supports interleaved and sequential layouts where applicable, converts between formats, and manipulates sequence sets (e.g., filtering by patterns and computing consensus sequences from alignments). Also includes functions to download nucleotide records from NCBI by accession.
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4.77 score 6 stars 2 dependents 13 scripts 1.2k 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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4.51 score 16 stars 40 scripts 292 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 208 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
4.20 score 16 scripts 300 downloadswikiprofiler - 'WikiPathway' Based Data Integration and Visualization
Queries online 'WikiPathway' graphics and allows mapping user data (e.g., expression values) on the graph. The package designs a grammar of graphic syntax that using pipe operator to add graphic layer.
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3.95 score 6 stars 7 scripts 548 downloadsmirrorselect - Test CRAN/Bioconductor Mirror Speed
Testing CRAN and Bioconductor mirror speed by recording download time of 'src/base/COPYING' (for CRAN) and 'packages/release/bioc/html/ggtree.html' (for Bioconductor).
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3.60 score 8 stars 1 scripts 174 downloadsplotbb - Grammar of Graphics for 'base' Plot
A grammar of graphics framework built on 'base' graphics. It provides a 'bbplot' object and a '+' operator to incrementally compose plots from data, aesthetic mappings and layers, then render them using the base plotting system. The package includes common geometric layers (points, lines, segments, bars, histograms, boxplots and tiles), scales for color and other aesthetics, legends, faceting, themes, and significance annotations.
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quarto
2.82 score 22 scripts 175 downloads