Circos plots facilitates the visualization of sequencing data and relevant genomic information. They are often used to integrate large amount of genomic data for one or multiple samples to emphasize particularities, similarities or differences, in a single graphical representation.
Displays large volumes of genomic rearrangement data. Circos is a visualization tool that applies a circular ideogram layout to display relationships between genomic intervals. The software provides a scalable means to illustrate relationships between genomic positions and is designed to allow flexible and easy rearrangement of elements in the image. It also contains several tools to help analyze, filter, and format data.
Allows visualization of genomic data in a circular layout. circlize implements basic low-level graphics functions, allowing users to implement more complicated graphics. The software is useful in visualizing and deciphering genomic information.
Permits users to visualize and explore genomics annotations and high-throughput data. ggbio provides applications to create both typical and non-typical biological plots for genomic data. This package supports both the convenient construction of typical genomic plots, while simultaneously supporting the invention of new types of plots from low-level building blocks.
A data integration framework for translating fragmented large-scale data into testable predictions. The Anduril framework allows rapid integration of heterogeneous data with state-of-the-art computational methods and existing knowledge in bio-databases. Anduril automatically generates thorough summary reports and a website that shows the most relevant features of each gene at a glance, allows sorting of data based on different parameters, and provides direct links to more detailed data on genes, transcripts or genomic regions. Anduril is open-source; all methods and documentation are freely available.
Assists users in obtaining genomic features from transcriptomic sequencing data, for any genome. MAP-RSeq is a comprehensive computational workflow, to align, assess and report multiple genomic features from paired-end RNA-Seq data. It uses a variety of freely available bioinformatics tools along with in-house developed methods using Perl, Python, R, and Java. This application is available in two versions: (i) a single threaded that runs on a virtual machine (VM) and (ii) a multi-threaded designed to run on a cluster environment.