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 2 months ago

annotationclusteringgenesetenrichmentgokeggmultiplecomparisonpathwaysreactomevisualizationenrichment-analysisgsea

17.09 score 1.0k 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 3 months ago

alignmentannotationclusteringdataimportmultiplesequencealignmentphylogeneticsreproducibleresearchsoftwarevisualizationannotationsggplot2phylogenetic-trees

16.94 score 850 stars 110 dependents 5.1k scripts 36k 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 3 months ago

annotationgoclusteringpathwaysnetworksoftwarebioinformaticsgene-ontologysemantic-similaritycpp

14.24 score 63 stars 67 dependents 708 scripts 30k downloads

scatterpie - Scatter Pie Plot

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

Last updated 14 days ago

13.51 score 61 stars 66 dependents 820 scripts 20k 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 6 months ago

phylogenetic-treetidyversetree-data

13.40 score 53 stars 129 dependents 542 scripts 25k 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 3 months ago

annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics

13.05 score 231 stars 5 dependents 1.6k scripts 3.3k 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 3 months ago

softwareannotationclusteringdataimportdatarepresentationalignmentmultiplesequencealignmentphylogeneticsexporterparserphylogenetic-trees

12.53 score 99 stars 123 dependents 1.3k scripts

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 15 days ago

11.99 score 101 stars 118 dependents 490 scripts 37k 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 5 days ago

10.56 score 18 stars 150 dependents 67 scripts 42k 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).

Last updated 3 months ago

visualizationmicrobiomesoftwaremultiplecomparisonfeatureextractionmicrobiome-analysismicrobiome-data

9.76 score 183 stars 1 dependents 126 scripts 697 downloads

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

Miscellaneous functions commonly used by 'YuLab-SMU'.

Last updated 14 days ago

9.75 score 32 stars 222 dependents 21 scripts 42k 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'.

Last updated 3 months ago

softwarevisualizationphylogeneticsannotation

9.70 score 89 stars 3 dependents 406 scripts 1.5k 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

9.59 score 42 stars 3 dependents 454 scripts 989 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 14 days ago

axis-breakcut-plotggbreakggplot2wrap-plot

9.49 score 132 stars 1 dependents 956 scripts 4.1k 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 1 months ago

softwarevisualizationalignmentannotationmultiplesequencealignment

9.34 score 206 stars 2 dependents 198 scripts 859 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 3 months ago

dimensionreductiongeneexpressionsinglecellsoftwarespatialtranscriptomicsvisualizationopenblascppopenmp

7.59 score 47 stars 18 scripts 178 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 3 months ago

microbiomesoftwarevisualizationkegg

6.79 score 37 stars 22 scripts 258 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 12 months ago

6.47 score 14 stars 1 dependents 71 scripts 896 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 11 months ago

molecular-clockphylogeneticsshiny-app

6.16 score 9 stars 7 scripts 177 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.

Last updated 3 months ago

geneexpressiondifferentialexpressionrnaseqcopynumbervariationmicroarraysoftwarednamethylationdifferentialmethylationsnpatacseqmethylationarray

5.96 score 24 stars 19 scripts 354 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 12 months ago

5.94 score 6 stars 3 dependents 8 scripts 558 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 3 months ago

annotationvisualizationphylogeneticssoftware

5.86 score 5 stars 12 scripts 107 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 2 months ago

5.80 score 53 stars 12 scripts 646 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 2 years ago

4.89 score 13 stars 60 scripts 767 downloads

MMINP - 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.

Last updated 2 years ago

metabolite-predictionmetabolitesmicrobes

4.81 score 13 stars 9 scripts 114 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 4 months ago

4.71 score 17 stars 20 scripts 194 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 1 months ago

4.38 score 8 stars 433 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 5 months ago

4.35 score 5 stars 5 scripts 143 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 5 months ago

3.60 score 8 stars 1 scripts 135 downloads