Assists users in plotting data. gplots is an R package that gathers a wide range of functionalities which permit (i) to calculate and plot locally summary function, (ii) to manipulate colors, (iii) to display Open Office style plots or (iv) to plot a matrix where each cell contains a dot whose size reflects the relative magnitude of the elements or Venn diagrams.
Provides a novel navigation tool for exploring hierarchical feature data that is coupled with multiple data visualizations including heatmaps, stacked bar charts, and scatter plots. Metaviz is a web browser-based tool for interactive visualization and exploration of metagenomic sequencing data. It also supports common data exploration techniques, including PCA scatter plots to interpret variability in the dataset and alpha diversity boxplots for examining ecological community composition.
Derives genome-based predictions from high-throughput genotyping and large-scale phenotyping data. synbreed contains a comprehensive collection of functions required to fit and cross-validate genomic prediction models. It offers a comprehensive collection of methods required in the analysis of genomic prediction data. synbreed is a valuable tool for the education of young scientists and breeders.
Creates heatmaps to represent complex datasets. superheat enables visual exploration of several types of data, adding to the heatmap a response variable as a scatterplot, and correlation information such as text information. This application can handle sets including multiple data types and furnishes features for extension and customization of the produced maps. It aims to assist users in analysis decision.
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.
Supplies a platform dedicated to the visualization and analyses of data belonging to diverse file formats and experimental protocols. metaseq is a library with the aim of furnishing: (i) a unified interface for ChIP-seq, RNA-seq, RNA immunoprecipitation and sequencing (RIP-seq) experiments, (ii) a mean for converting genomic signal into NumPy arrays as well as (iii) an access to data from commonly used file format such as BAM or GFF.
Allows users to select, aggregate, and visualize metagenomic data. ASAR enables researchers to develop a meaningful view of their data. The software consists of a main panel with seven tabs and a control panel, which provides a set of parameter selectors for controlling the displayed tab content. It can perform taxonomic and functional analyses simultaneously, by subsetting and aggregating abundance data at various levels of taxonomic and functional hierarchies.