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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>.

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16.30 score 1.0k stars 281 dependents 24k scripts 49k 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.

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11.69 score 17 stars 214 dependents 829 scripts 36k 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>.

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6.87 score 4 stars 124 scripts 622 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.

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6.64 score 4 stars 2 dependents 365 scripts 1.0k 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.

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6.57 score 159 stars 47 scripts 587 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.

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softwareinfrastructure

5.71 score 27 stars 38 scripts 497 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.

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cpp

4.00 score 1 stars 20 scripts 341 downloads