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.
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softwarevisualizationsequencingclusteringcomplex-heatmapsheatmap
16.06 score 1.5k stars 195 dependents 34k scriptsGetoptLong - 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.
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11.75 score 17 stars 194 dependents 739 scripts 51k 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.
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softwarevisualizationsequencinggenomeannotationcoveragecpp
10.83 score 201 stars 2 dependents 621 scriptsGlobalOptions - 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.
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10.18 score 9 stars 259 dependents 66 scripts 66k 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.
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genesetenrichmentgopathwayssoftwaresequencingwholegenomegenomeannotationcoveragecpp
10.06 score 98 stars 1 dependents 525 scriptsInteractiveComplexHeatmap - 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.
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softwarevisualizationsequencinginteractive-heatmaps
8.82 score 141 stars 4 dependents 185 scripts 1.0k 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.
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softwarevisualizationsequencing
8.50 score 43 stars 1 dependents 61 scripts 642 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.
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softwarevisualizationgoclusteringgenesetenrichment
8.24 score 126 stars 308 scriptsHilbertCurve - 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.
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softwarevisualizationsequencingcoveragegenomeannotationcpp
7.68 score 44 stars 78 scriptscola - 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.
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clusteringgeneexpressionclassificationsoftwareconsensus-clusteringcpp
7.68 score 64 stars 165 scriptssimona - 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.
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softwareannotationgobiomedicalinformaticscpp
7.15 score 18 stars 2 dependents 44 scriptsspiralize - 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.
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7.05 score 159 stars 1 dependents 47 scripts 768 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.
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6.81 score 4 stars 2 dependents 335 scripts 1.6k 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.
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softwareinfrastructure
5.77 score 27 stars 44 scripts 597 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.
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softwarepathwaysbiocartavisualization
5.26 score 11 stars 11 scripts 258 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.
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cpp
4.00 score 1 stars 20 scripts 477 downloads