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 4 months ago

annotationclusteringgenesetenrichmentgokeggmultiplecomparisonpathwaysreactomevisualizationenrichment-analysisgsea

17.03 score 1.1k stars 48 dependents 11k scripts 34k 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.

Last updated 5 months ago

alignmentannotationclusteringdataimportmultiplesequencealignmentphylogeneticsreproducibleresearchsoftwarevisualizationannotationsggplot2phylogenetic-trees

16.83 score 871 stars 109 dependents 5.1k scripts 35k downloads

enrichplot - 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 3 months ago

annotationgenesetenrichmentgokeggpathwayssoftwarevisualizationenrichment-analysispathway-analysis

15.71 score 239 stars 58 dependents 3.1k scripts 31k downloads

DOSE - 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 5 months ago

annotationvisualizationmultiplecomparisongenesetenrichmentpathwayssoftwaredisease-ontologyenrichment-analysissemantic-similarity

14.97 score 119 stars 61 dependents 2.0k scripts 29k downloads

GOSemSim - 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 5 months ago

annotationgoclusteringpathwaysnetworksoftwarebioinformaticsgene-ontologysemantic-similaritycpp

14.12 score 63 stars 68 dependents 708 scripts 28k downloads

scatterpie - Scatter Pie Plot

Creates scatterpie plots, especially useful for plotting pies on a map.

Last updated 3 months ago

13.60 score 62 stars 68 dependents 820 scripts 26k downloads

tidytree - 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 8 months ago

phylogenetic-treetidyversetree-data

13.36 score 56 stars 128 dependents 584 scripts 30k downloads

ggplotify - 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

13.23 score 108 stars 174 dependents 2.0k scripts 43k 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.

Last updated 5 months ago

annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics

13.05 score 233 stars 5 dependents 1.6k scripts 3.7k 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 5 months ago

softwareannotationclusteringdataimportdatarepresentationalignmentmultiplesequencealignmentphylogeneticsexporterparserphylogenetic-trees

12.46 score 102 stars 122 dependents 1.3k scripts

ReactomePA - 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 5 months ago

pathwaysvisualizationannotationmultiplecomparisongenesetenrichmentreactomeenrichment-analysisreactome-pathway-analysisreactomepa

12.25 score 40 stars 7 dependents 1.5k scripts 4.1k downloads

aplot - 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 months ago

12.25 score 103 stars 118 dependents 520 scripts 62k downloads

hexSticker - Create Hexagon Sticker in R

Helper functions for creating reproducible hexagon sticker purely in R.

Last updated 2 months ago

ggplot2hexagon-stickerlogostickersvisualization

11.79 score 773 stars 8 dependents 1.3k scripts 940 downloads

ggimage - Use Image in 'ggplot2'

Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.

Last updated 1 years ago

ggplot2imagevisualization

11.12 score 172 stars 20 dependents 2.4k scripts 7.2k downloads

shadowtext - 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 2 months ago

10.65 score 37 stars 10 dependents 552 scripts 12k downloads

ggfun - Miscellaneous Functions for 'ggplot2'

Useful functions and utilities for 'ggplot' object (e.g., geometric layers, themes, and utilities to edit the object).

Last updated 17 days ago

10.53 score 18 stars 152 dependents 58 scripts 51k downloads

yulab.utils - Supporting Functions for Packages Maintained by 'YuLab-SMU'

Miscellaneous functions commonly used by 'YuLab-SMU'.

Last updated 19 days ago

9.94 score 33 stars 228 dependents 21 scripts 68k 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>).

Last updated 2 months ago

axis-breakcut-plotggbreakggplot2wrap-plot

9.81 score 137 stars 1 dependents 956 scripts 8.3k downloads

scholar - 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

9.60 score 42 stars 3 dependents 468 scripts 997 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 3 months ago

softwarevisualizationalignmentannotationmultiplesequencealignment

9.35 score 210 stars 2 dependents 196 scripts 896 downloads

badger - Badge for R Package

Query information and generate badge for using in README and GitHub Pages.

Last updated 9 months ago

badge

8.92 score 197 stars 5 dependents 225 scripts 1.1k downloads

emojifont - 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

8.50 score 67 stars 3 dependents 900 scripts 1.2k 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'.

Last updated 5 months ago

dimensionreductiongeneexpressionsinglecellsoftwarespatialtranscriptomicsvisualizationopenblascppopenmp

7.59 score 47 stars 18 scripts 216 downloads

dlstats - 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

7.43 score 14 stars 7 dependents 56 scripts 1.1k downloads

meshes - 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 5 months ago

annotationclusteringmultiplecomparisonsoftwareenrichment-analysismedical-subject-headingssemantic-similarity

7.19 score 12 stars 43 scripts 415 downloads

meme - 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 341 downloads

ggtangle - 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 4 months ago

6.87 score 1 stars 59 dependents 3 scripts 17k 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.

Last updated 5 months ago

microbiomesoftwarevisualizationkegg

6.80 score 38 stars 22 scripts 288 downloads

rvcheck - R/Package Version Check

Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').

Last updated 3 years ago

6.56 score 23 stars 7 dependents 45 scripts 1.7k downloads

tidydr - 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 948 downloads

seqcombo - Visualization Tool for Genetic Reassortment

Provides useful functions for visualizing virus reassortment events.

Last updated 5 months ago

alignmentsoftwarevisualization

5.92 score 21 stars 4 scripts 221 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.

Last updated 5 months ago

annotationvisualizationphylogeneticssoftware

5.80 score 5 stars 12 scripts 164 downloads

seqmagick - 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 787 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.

Last updated 5 months ago

5.49 score 52 stars 10 scripts 564 downloads

shinyTempSignal - 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 1 years ago

molecular-clockphylogeneticsshiny-app

5.26 score 9 stars 7 scripts 192 downloads

gson - 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

5.07 score 52 dependents 38 scripts 20k downloads

TDbook - 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 3 years ago

4.88 score 13 stars 59 scripts 918 downloads

wget - 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 6 months ago

4.73 score 17 stars 21 scripts 229 downloads

aplotExtra - 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 4 months ago

4.20 score 8 stars 315 downloads

ggtreeDendro - 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 5 months ago

clusteringclassificationdecisiontreephylogeneticsvisualization

4.18 score 10 scripts 207 downloads

wikiprofiler - '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 7 months ago

4.18 score 5 stars 5 scripts 140 downloads

mirrorselect - 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 7 months ago

3.60 score 8 stars 1 scripts 144 downloads

plotbb - 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 4 years ago

2.08 score 12 scripts 141 downloads