ComplexHeatmap - Make Complex Heatmaps

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

Last updated 5 months ago

softwarevisualizationsequencingclusteringcomplex-heatmapsheatmap

16.94 score 1.4k stars 155 dependents 16k scripts 25k downloads

circlize - Circular Visualization

Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data. The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.

Last updated 1 years ago

15.62 score 983 stars 213 dependents 10k scripts 32k downloads

GetoptLong - Parsing Command-Line Arguments and Simple Variable Interpolation

This is a command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptations for easier use in R. It also provides a simple way for variable interpolation in R.

Last updated 3 years ago

11.08 score 17 stars 160 dependents 478 scripts 20k downloads

EnrichedHeatmap - Making Enriched Heatmaps

Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.

Last updated 5 months ago

softwarevisualizationsequencinggenomeannotationcoveragecpp

10.87 score 190 stars 1 dependents 330 scripts 1.1k downloads

rGREAT - GREAT Analysis - Functional Enrichment on Genomic Regions

GREAT (Genomic Regions Enrichment of Annotations Tool) is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm (the local GREAT analysis), also it supports directly interacting with the GREAT web service (the online GREAT analysis). Both analysis can be viewed by a Shiny application. rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions.

Last updated 17 days ago

genesetenrichmentgopathwayssoftwaresequencingwholegenomegenomeannotationcoveragecpp

9.96 score 86 stars 1 dependents 320 scripts 1.1k downloads

GlobalOptions - Generate Functions to Get or Set Global Options

It provides more configurations on the option values such as validation and filtering on the values, making options invisible or private.

Last updated 9 months ago

9.54 score 9 stars 221 dependents 40 scripts 29k downloads

InteractiveComplexHeatmap - Make Interactive Complex Heatmaps

This package can easily make heatmaps which are produced by the ComplexHeatmap package into interactive applications. It provides two types of interactivities: 1. on the interactive graphics device, and 2. on a Shiny app. It also provides functions for integrating the interactive heatmap widgets for more complex Shiny app development.

Last updated 5 months ago

softwarevisualizationsequencinginteractive-heatmaps

9.52 score 134 stars 4 dependents 128 scripts 792 downloads

gtrellis - Genome Level Trellis Layout

Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.

Last updated 5 months ago

softwarevisualizationsequencing

8.24 score 39 stars 1 dependents 37 scripts 449 downloads

simplifyEnrichment - Simplify Functional Enrichment Results

A new clustering algorithm, "binary cut", for clustering similarity matrices of functional terms is implemeted in this package. It also provides functions for visualizing, summarizing and comparing the clusterings.

Last updated 5 months ago

softwarevisualizationgoclusteringgenesetenrichment

8.02 score 113 stars 196 scripts 1.6k downloads

cola - A Framework for Consensus Partitioning

Subgroup classification is a basic task in genomic data analysis, especially for gene expression and DNA methylation data analysis. It can also be used to test the agreement to known clinical annotations, or to test whether there exist significant batch effects. The cola package provides a general framework for subgroup classification by consensus partitioning. It has the following features: 1. It modularizes the consensus partitioning processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to straightforward compare results. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It automatically generates detailed reports for the complete analysis. 6. It allows applying consensus partitioning in a hierarchical manner.

Last updated 2 months ago

clusteringgeneexpressionclassificationsoftwareconsensus-clusteringcpp

7.49 score 61 stars 112 scripts 285 downloads

HilbertCurve - Making 2D Hilbert Curve

Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the locality. This package aims to provide an easy and flexible way to visualize data through Hilbert curve.

Last updated 5 months ago

softwarevisualizationsequencingcoveragegenomeannotationcpp

7.45 score 42 stars 48 scripts 296 downloads

spiralize - Visualize Data on Spirals

It visualizes data along an Archimedean spiral <https://en.wikipedia.org/wiki/Archimedean_spiral>, makes so-called spiral graph or spiral chart. It has two major advantages for visualization: 1. It is able to visualize data with very long axis with high resolution. 2. It is efficient for time series data to reveal periodic patterns.

Last updated 10 months ago

7.37 score 149 stars 3 dependents 35 scripts 596 downloads

pkgndep - Analyze Dependency Heaviness of R Packages

A new metric named 'dependency heaviness' is proposed that measures the number of additional dependency packages that a parent package brings to its child package and are unique to the dependency packages imported by all other parents. The dependency heaviness analysis is visualized by a customized heatmap. The package is described in <doi:10.1093/bioinformatics/btac449>. We have also performed the dependency heaviness analysis on the CRAN/Bioconductor package ecosystem and the results are implemented as a web-based database which provides comprehensive tools for querying dependencies of individual R packages. The systematic analysis on the CRAN/Bioconductor ecosystem is described in <doi:10.1016/j.jss.2023.111610>. From 'pkgndep' version 2.0.0, the heaviness database includes snapshots of the CRAN/Bioconductor ecosystems for many old R versions.

Last updated 27 days ago

6.75 score 47 stars 30 scripts 470 downloads

simona - Semantic Similarity on Bio-Ontologies

This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.

Last updated 5 months ago

softwareannotationgobiomedicalinformaticscpp

6.62 score 17 stars 1 dependents 27 scripts 322 downloads

CePa - Centrality-Based Pathway Enrichment

This package aims to find significant pathways through network topology information. It has several advantages compared with current pathway enrichment tools. First, pathway node instead of single gene is taken as the basic unit when analysing networks to meet the fact that genes must be constructed into complexes to hold normal functions. Second, multiple network centrality measures are applied simultaneously to measure importance of nodes from different aspects to make a full view on the biological system. CePa extends standard pathway enrichment methods, which include both over-representation analysis procedure and gene-set analysis procedure. <https://doi.org/10.1093/bioinformatics/btt008>.

Last updated 4 years ago

6.53 score 3 stars 75 scripts 428 downloads

bsub - Submitter and Monitor of the 'LSF Cluster'

It submits R code/R scripts/shell commands to 'LSF cluster' (<https://en.wikipedia.org/wiki/Platform_LSF>, the 'bsub' system) without leaving R. There is also an interactive 'shiny' application for monitoring job status.

Last updated 16 days ago

softwareinfrastructure

6.01 score 25 stars 27 scripts 286 downloads

colorRamp2 - Generate Color Mapping Functions

A color mapping is generated according to the break values and corresponding colors. Other colors are generated by interpolating in a certain color space.

Last updated 2 years ago

5.67 score 1 stars 2 dependents 155 scripts 937 downloads

BioCartaImage - BioCarta Pathway Images

The core functionality of the package is to provide coordinates of genes on the BioCarta pathway images and to provide methods to add self-defined graphics to the genes of interest.

Last updated 5 months ago

softwarepathwaysbiocartavisualization

5.04 score 11 stars 6 scripts 143 downloads

sfcurve - 2x2, 3x3 and Nxn Space-Filling Curves

Implementation of all possible forms of 2x2 and 3x3 space-filling curves, i.e., the generalized forms of the Hilbert curve <https://en.wikipedia.org/wiki/Hilbert_curve>, the Peano curve <https://en.wikipedia.org/wiki/Peano_curve> and the Peano curve in the meander type (Figure 5 in <https://eudml.org/doc/141086>). It can generates nxn curves expanded from any specific level-1 units. It also implements the H-curve and the three-dimensional Hilbert curve.

Last updated 6 months ago

cpp

4.66 score 1 stars 13 scripts 138 downloads