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.
Last updated 3 months ago
annotationclusteringgenesetenrichmentgokeggmultiplecomparisonpathwaysreactomevisualizationenrichment-analysisgsea
17.07 score 1.1k stars 48 dependents 11k scripts 34k 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.
Last updated 4 months ago
alignmentannotationclusteringdataimportmultiplesequencealignmentphylogeneticsreproducibleresearchsoftwarevisualizationannotationsggplot2phylogenetic-trees
16.94 score 858 stars 109 dependents 5.1k scripts 36k downloadsenrichplot - 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.
Last updated 1 months ago
annotationgenesetenrichmentgokeggpathwayssoftwarevisualizationenrichment-analysispathway-analysis
15.73 score 239 stars 58 dependents 3.1k scripts 31k 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.
Last updated 4 months ago
annotationvisualizationmultiplecomparisongenesetenrichmentpathwayssoftwaredisease-ontologyenrichment-analysissemantic-similarity
15.01 score 118 stars 61 dependents 2.0k scripts 29k 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.
Last updated 4 months ago
annotationgoclusteringpathwaysnetworksoftwarebioinformaticsgene-ontologysemantic-similaritycpp
14.20 score 63 stars 68 dependents 708 scripts 30k downloadsscatterpie - Scatter Pie Plot
Creates scatterpie plots, especially useful for plotting pies on a map.
Last updated 1 months ago
13.54 score 61 stars 68 dependents 820 scripts 20k 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.
Last updated 7 months ago
phylogenetic-treetidyversetree-data
13.30 score 54 stars 130 dependents 542 scripts 19k 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.
Last updated 4 months ago
annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics
13.06 score 233 stars 5 dependents 1.6k scripts 3.3k 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.
Last updated 1 years ago
baseplotggplot2gridlatticeupsetrvcd
13.05 score 109 stars 168 dependents 2.0k scripts 29k 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.
Last updated 4 months ago
softwareannotationclusteringdataimportdatarepresentationalignmentmultiplesequencealignmentphylogeneticsexporterparserphylogenetic-trees
12.49 score 100 stars 122 dependents 1.3k scriptsReactomePA - 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.
Last updated 4 months ago
pathwaysvisualizationannotationmultiplecomparisongenesetenrichmentreactomeenrichment-analysisreactome-pathway-analysisreactomepa
12.31 score 40 stars 7 dependents 1.5k scripts 4.1k 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.
Last updated 1 days ago
12.05 score 102 stars 118 dependents 520 scripts 40k downloadshexSticker - Create Hexagon Sticker in R
Helper functions for creating reproducible hexagon sticker purely in R.
Last updated 23 days ago
ggplot2hexagon-stickerlogostickersvisualization
11.91 score 770 stars 8 dependents 1.3k scripts 932 downloadsggimage - Use Image in 'ggplot2'
Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.
Last updated 1 years ago
ggplot2imagevisualization
11.00 score 172 stars 19 dependents 2.4k scripts 5.8k 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.
Last updated 22 days ago
10.66 score 38 stars 9 dependents 552 scripts 10k downloadsggfun - Miscellaneous Functions for 'ggplot2'
Useful functions and utilities for 'ggplot' object (e.g., geometric layers, themes, and utilities to edit the object).
Last updated 1 months ago
10.41 score 18 stars 151 dependents 58 scripts 46k 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>).
Last updated 16 days ago
axis-breakcut-plotggbreakggplot2wrap-plot
9.90 score 133 stars 1 dependents 956 scripts 7.0k downloadsyulab.utils - Supporting Functions for Packages Maintained by 'YuLab-SMU'
Miscellaneous functions commonly used by 'YuLab-SMU'.
Last updated 23 days ago
9.89 score 32 stars 224 dependents 21 scripts 63k 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.
Last updated 1 years ago
9.59 score 42 stars 3 dependents 454 scripts 896 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.
Last updated 2 months ago
softwarevisualizationalignmentannotationmultiplesequencealignment
9.34 score 209 stars 2 dependents 196 scripts 896 downloadsbadger - Badge for R Package
Query information and generate badge for using in README and GitHub Pages.
Last updated 7 months ago
badge
9.04 score 197 stars 5 dependents 225 scripts 873 downloadsemojifont - Emoji and Font Awesome in Graphics
An implementation of using emoji and fontawesome for using in both base and 'ggplot2' graphics.
Last updated 4 years ago
emojifont-awesomeggplot2visualization
8.43 score 67 stars 3 dependents 900 scripts 856 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'.
Last updated 4 months ago
dimensionreductiongeneexpressionsinglecellsoftwarespatialtranscriptomicsvisualizationopenblascppopenmp
7.59 score 47 stars 18 scripts 215 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/>.
Last updated 1 years ago
7.39 score 14 stars 7 dependents 56 scripts 966 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.
Last updated 4 months ago
annotationclusteringmultiplecomparisonsoftwareenrichment-analysismedical-subject-headingssemantic-similarity
7.25 score 11 stars 43 scripts 355 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.
Last updated 4 years ago
gridmemevisualization
7.08 score 45 stars 54 scripts 282 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.
Last updated 4 months ago
microbiomesoftwarevisualizationkegg
6.79 score 37 stars 22 scripts 281 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.
Last updated 2 months ago
6.75 score 1 stars 59 dependents 3 scripts 13k downloadsrvcheck - R/Package Version Check
Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').
Last updated 3 years ago
6.50 score 23 stars 7 dependents 45 scripts 1.4k 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.
Last updated 1 years ago
6.47 score 14 stars 1 dependents 71 scripts 797 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.
Last updated 12 months ago
molecular-clockphylogeneticsshiny-app
5.95 score 9 stars 7 scripts 240 downloadsseqcombo - Visualization Tool for Genetic Reassortment
Provides useful functions for visualizing virus reassortment events.
Last updated 4 months ago
alignmentsoftwarevisualization
5.92 score 21 stars 4 scripts 217 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.
Last updated 4 months ago
annotationvisualizationphylogeneticssoftware
5.86 score 5 stars 12 scripts 134 downloadsseqmagick - Sequence Manipulation Utilities
Supports reading and writing sequences for different formats (currently interleaved and sequential formats for 'FASTA' and 'PHYLIP'), file conversion, and manipulation (e.g. filter sequences that contain specify pattern, export consensus sequence from an alignment).
Last updated 1 years ago
5.64 score 6 stars 3 dependents 8 scripts 652 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).
Last updated 2 years ago
4.88 score 13 stars 59 scripts 766 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.
Last updated 2 years ago
4.87 score 52 dependents 38 scripts 12k 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.
Last updated 5 months ago
4.71 score 17 stars 20 scripts 194 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.
Last updated 6 months ago
4.35 score 5 stars 5 scripts 169 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.
Last updated 4 months ago
clusteringclassificationdecisiontreephylogeneticsvisualization
4.30 score 10 scripts 175 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.
Last updated 2 months ago
4.20 score 8 stars 309 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).
Last updated 6 months ago
3.60 score 8 stars 1 scripts 153 downloadsplotbb - Grammar of Graphics for 'base' Plot
Proof of concept for implementing grammar of graphics using base plot. The bbplot() function initializes a 'bbplot' object to store input data, aesthetic mapping, a list of layers and theme elements. The object will be rendered as a graphic using base plot command if it is printed.
Last updated 3 years ago
2.08 score 12 scripts 187 downloads