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 4 months ago
softwarevisualizationsequencingclusteringcomplex-heatmapsheatmap
15.93 score 1.3k stars 149 dependents 16k scripts 25k downloadscirclize - 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
15.53 score 981 stars 206 dependents 10k scripts 27k downloadsGetoptLong - 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 2 years ago
10.90 score 17 stars 158 dependents 470 scripts 14k downloadsEnrichedHeatmap - 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 4 months ago
softwarevisualizationsequencinggenomeannotationcoveragecpp
10.86 score 190 stars 1 dependents 330 scripts 1.1k downloadsrGREAT - 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 4 months ago
genesetenrichmentgopathwayssoftwaresequencingwholegenomegenomeannotationcoveragecpp
10.05 score 86 stars 1 dependents 320 scripts 1.0k downloadsInteractiveComplexHeatmap - 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 4 months ago
softwarevisualizationsequencinginteractive-heatmaps
9.68 score 131 stars 4 dependents 128 scripts 715 downloadsGlobalOptions - 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 8 months ago
9.40 score 9 stars 213 dependents 40 scripts 22k downloadsgtrellis - 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 4 months ago
softwarevisualizationsequencing
8.24 score 39 stars 1 dependents 37 scripts 422 downloadssimplifyEnrichment - 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 4 months ago
softwarevisualizationgoclusteringgenesetenrichment
8.02 score 113 stars 196 scripts 1.6k downloadsspiralize - 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 8 months ago
7.67 score 148 stars 3 dependents 35 scripts 625 downloadscola - 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 12 days ago
clusteringgeneexpressionclassificationsoftwareconsensus-clusteringcpp
7.61 score 61 stars 112 scripts 271 downloadsHilbertCurve - 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 4 months ago
softwarevisualizationsequencingcoveragegenomeannotationcpp
7.44 score 41 stars 48 scripts 260 downloadssimona - 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 4 months ago
softwareannotationgobiomedicalinformaticscpp
6.66 score 16 stars 1 dependents 27 scripts 298 downloadscolorRamp2 - 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 960 downloadsBioCartaImage - 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 4 months ago
softwarepathwaysbiocartavisualization
5.00 score 10 stars 6 scripts 143 downloadsbsub - 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 8 months ago
softwareinfrastructure
4.83 score 25 stars 27 scripts 240 downloadssfcurve - 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 5 months ago
cpp
4.66 score 1 stars 13 scripts 168 downloads