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
15.89 score 1.2k stars 48 dependents 23k scriptsggtree - 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
15.81 score 928 stars 114 dependents 10.0k scriptsscatterpie - Scatter Pie Plot
Creates scatterpie plots, especially useful for plotting pies on a map.
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13.68 score 67 stars 71 dependents 1.2k scripts 50k 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
13.23 score 61 stars 140 dependents 1.1k scripts 70k 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
13.14 score 72 stars 70 dependents 1.0k scriptsChIPseeker - 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
12.73 score 257 stars 5 dependents 3.1k scriptsaplot - 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 129 stars 126 dependents 936 scripts 82k 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
12.17 score 104 stars 131 dependents 2.8k scriptsggimage - Use Image in 'ggplot2'
Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.
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ggplot2imagevisualization
12.14 score 178 stars 22 dependents 4.0k scripts 7.3k 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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quarto
11.43 score 18 stars 167 dependents 153 scripts 64k 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
10.81 score 148 stars 2 dependents 2.3k scripts 7.7k 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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quarto
10.56 score 52 stars 2 dependents 562 scripts 2.9k downloadsyulab.utils - Supporting Functions for Packages Maintained by 'YuLab-SMU'
Miscellaneous functions commonly used by 'YuLab-SMU'.
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10.47 score 38 stars 264 dependents 52 scripts 79k downloadsggtreeExtra - 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'.
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softwarevisualizationphylogeneticsannotation
10.26 score 98 stars 2 dependents 684 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
9.95 score 218 stars 1 dependents 303 scripts 1000 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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9.64 score 15 stars 60 dependents 202 scripts 26k downloadsMicrobiotaProcess - 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).
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visualizationmicrobiomesoftwaremultiplecomparisonfeatureextractionmicrobiome-analysismicrobiome-data
9.50 score 195 stars 225 scripts 856 downloadsaisdk - Unified Interface for AI Model Providers
A production-grade AI toolkit for R featuring a layered architecture (Specification, Utilities, Providers, Core), request interception support, robust error handling with exponential retry delays, support for multiple AI model providers ('OpenAI', 'Anthropic', etc.), local small language model inference, distributed 'MCP' ecosystem, multi-agent orchestration, progressive knowledge loading through skills, and a global skill store for sharing AI capabilities.
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9.08 score 68 stars 51 dependents 34 scripts 17k 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
7.40 score 12 stars 56 scriptsMicrobiomeProfiler - 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
7.36 score 42 stars 44 scripts 356 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
7.31 score 51 stars 38 scriptsGeoTcgaData - Processing Various Types of Data on GEO and TCGA
Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.
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geneexpressiondifferentialexpressionrnaseqcopynumbervariationmicroarraysoftwarednamethylationdifferentialmethylationsnpatacseqmethylationarray
5.88 score 28 stars 27 scriptsseqmagick - 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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5.67 score 6 stars 2 dependents 15 scripts 1.1k 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
5.50 score 7 stars 6 scripts 616 downloadsSVP - Predicting cell states and their variability in single-cell or spatial omics data
SVP uses the distance between cells and cells, features and features, cells and features in the space of MCA to build nearest neighbor graph, then uses random walk with restart algorithm to calculate the activity score of gene sets (such as cell marker genes, kegg pathway, go ontology, gene modules, transcription factor or miRNA target sets, reactome pathway, ...), which is then further weighted using the hypergeometric test results from the original expression matrix. To detect the spatially or single cell variable gene sets or (other features) and the spatial colocalization between the features accurately, SVP provides some global and local spatial autocorrelation method to identify the spatial variable features. SVP is developed based on SingleCellExperiment class, which can be interoperable with the existing computing ecosystem.
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singlecellsoftwarespatialtranscriptomicsgenetargetgeneexpressiongenesetenrichmenttranscriptiongokeggopenblascppopenmp
5.38 score 12 stars 8 scriptsepiSeeker - 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
5.35 score 86 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 scriptsshinyTempSignal - 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 8 scripts 281 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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5.11 score 13 stars 98 scripts 537 downloadsMMINP - Microbe-Metabolite Interactions-Based Metabolic Profiles Predictor
Implements a computational framework to predict microbial community-based metabolic profiles with 'O2PLS' model. It provides procedures of model training and prediction. Paired microbiome and metabolome data are needed for modeling, and the trained model can be applied to predict metabolites of analogous environments using new microbial feature abundances.
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metabolite-predictionmetabolitesmicrobes
4.90 score 16 stars 10 scripts 317 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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4.60 score 16 stars 50 scripts 231 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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4.18 score 10 stars 1 scripts 299 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 516 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 180 downloads