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
softwarevisualizationsequencing
1.3k stars 10.92 score 20 dependencies 137 dependentsGlobalOptions - 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 2 months ago
9 stars 7.85 score 0 dependencies 199 dependentsGetoptLong - 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
16 stars 7.18 score 3 dependencies 146 dependentsEnrichedHeatmap - 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
softwarevisualizationsequencinggenomeannotationcoverage
185 stars 5.63 score 38 dependencies 1 dependentsspiralize - 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 3 months ago
142 stars 4.83 score 25 dependencies 2 dependentsInteractiveComplexHeatmap - 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
softwarevisualizationsequencing
123 stars 4.58 score 71 dependencies 3 dependentssimplifyEnrichment - 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
102 stars 4.22 score 73 dependenciesgtrellis - 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
39 stars 3.36 score 24 dependencies 1 dependentsHilbertCurve - 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
softwarevisualizationsequencingcoveragegenomeannotation
40 stars 2.97 score 26 dependenciesrGREAT - 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
genesetenrichmentgopathwayssoftwaresequencingwholegenomegenomeannotationcoverage
2.53 score 113 dependencies 2 dependentsbsub - 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 2 months ago
24 stars 2.36 score 25 dependenciessimona - 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 10 days ago
softwareannotationgobiomedicalinformatics
10 stars 2.00 score 58 dependenciesBioCartaImage - 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
11 stars 1.51 score 4 dependenciescolorRamp2 - 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
1 stars 1.08 score 1 dependencies 1 dependents