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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

18.00 score 1.2k stars 62 dependents 24k scripts 58k downloads

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.

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alignmentannotationclusteringdataimportmultiplesequencealignmentphylogeneticsreproducibleresearchsoftwarevisualizationannotationsggplot2phylogenetic-trees

17.66 score 935 stars 129 dependents 9.9k scripts 74k downloads

GOSemSim - 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 downloads

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.

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annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics

13.95 score 259 stars 7 dependents 3.5k scripts 5.8k downloads

scatterpie - 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 downloads

ggimage - 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 downloads

aplot - 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 downloads

ggfun - 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

11.30 score 18 stars 176 dependents 147 scripts 71k downloads

tidytree - 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 downloads

ggbreak - 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 downloads

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'.

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softwarevisualizationphylogeneticsannotation

10.78 score 99 stars 2 dependents 922 scripts 3.7k downloads

tidydr - 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 downloads

scholar - 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

10.49 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 downloads

yulab.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 downloads

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).

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visualizationmicrobiomesoftwaremultiplecomparisonfeatureextractionmicrobiome-analysismicrobiome-data

9.32 score 195 stars 224 scripts 908 downloads

aisdk - 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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9.32 score 76 stars 61 dependents 34 scripts 17k downloads

gson - 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 downloads

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'.

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dimensionreductiongeneexpressionsinglecellsoftwarespatialtranscriptomicsvisualizationopenblascppopenmp

7.52 score 51 stars 37 scripts 346 downloads

MicrobiomeProfiler - 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 downloads

meshes - 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 downloads

seqmagick - 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, and reads or writes gzip, bzip2 and xz compressed files transparently. Converts between formats, renames sequences via a two-column mapping, summarizes sequence counts, lengths, GC content and ambiguous characters, 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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6.75 score 6 stars 2 dependents 16 scripts 1.2k downloads

fanyi - Translate Words or Sentences via Online Translators

Useful functions to translate text for multiple languages using online translators. For example, by translating error messages and descriptive analysis results into a language familiar to the user, it enables a better understanding of the information, thereby reducing the barriers caused by language. It offers several helper functions to query gene information to help interpretation of interested genes (e.g., marker genes, differential expression genes), and provides utilities to translate 'ggplot' graphics. This package is not affiliated with any of the online translators. The developers do not take responsibility for the invoice it incurs when using this package, especially for exceeding the free quota.

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6.55 score 60 stars 99 scripts 528 downloads

GeoTcgaData - 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

5.92 score 27 stars 31 scripts 376 downloads

SVP - 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

5.56 score 12 stars 6 scripts 332 downloads

epiSeeker - 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.

Last updated

annotationchipseqsoftwarevisualizationmultiplecomparisoncoveragemotifannotationgeneregulation

5.38 score 223 downloads

ivolcano - 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

5.32 score 7 stars 4 scripts 421 downloads

ggtreeSpace - 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 downloads

wikiprofiler - 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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quarto

5.26 score 6 stars 412 downloads