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 24 days ago

softwarevisualizationsequencingclusteringcomplex-heatmapsheatmap

15.85 score 1.3k stars 147 packages 14k scripts 24k 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

15.55 score 969 stars 201 packages 9.6k 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 2 years ago

10.95 score 17 stars 152 packages 434 scripts 17k 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 24 days ago

softwarevisualizationsequencinggenomeannotationcoverage

10.81 score 187 stars 1 packages 318 scripts 1.0k 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 24 days ago

genesetenrichmentgopathwayssoftwaresequencingwholegenomegenomeannotationcoverage

10.22 score 85 stars 1 packages 316 scripts 1.0k 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 24 days ago

softwarevisualizationsequencinginteractive-heatmaps

9.52 score 127 stars 3 packages 122 scripts 683 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 5 months ago

9.46 score 9 stars 209 packages 40 scripts 26k 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 24 days ago

softwarevisualizationsequencing

8.24 score 39 stars 1 packages 37 scripts 378 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 24 days ago

softwarevisualizationgoclusteringgenesetenrichment

8.09 score 109 stars 175 scripts 1.4k 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 5 months ago

7.64 score 147 stars 2 packages 33 scripts 585 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 24 days ago

clusteringgeneexpressionclassificationsoftwareconsensus-clustering

7.46 score 59 stars 108 scripts 253 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 24 days ago

softwarevisualizationsequencingcoveragegenomeannotation

7.44 score 41 stars 48 scripts 256 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 24 days ago

softwareannotationgobiomedicalinformatics

6.86 score 15 stars 1 packages 27 scripts 194 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 1 years ago

6.42 score 45 stars 29 scripts 379 downloads

YAPSA - Yet Another Package for Signature Analysis

This package provides functions and routines for supervised analyses of mutational signatures (i.e., the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signature-specific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata.

Last updated 24 days ago

sequencingdnaseqsomaticmutationvisualizationclusteringgenomicvariationstatisticalmethodbiologicalquestion

6.41 score 57 scripts 426 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 3 years ago

6.35 score 2 stars 74 scripts 496 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

5.64 score 1 stars 2 packages 145 scripts 998 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 24 days ago

softwarepathwaysbiocartavisualization

5.00 score 10 stars 6 scripts 116 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 5 months ago

softwareinfrastructure

4.99 score 24 stars 27 scripts 235 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 2 months ago

4.66 score 1 stars 13 scripts 133 downloads