Heatmap creation software tools | Transcription data analysis
Heatmaps are one of the most commonly used representation tool for creation of complex pools of data. By coding numerical values into colors, heatmaps enable quick representation of quantitative differences in expression levels of biological data. Heatmaps are particularly useful for analysis of gene expression microarray data. Most heatmap representations are also combined with clustering methods to group genes and/or samples based on their expression patterns. Each gene is represented as a row and is color-coded to represent the intensity of its variation (either positive or negative) relative to a reference value. Biological samples are represented as columns in the grid. Here is a selection of heatmap creation software tools.
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.
Allows users to draw heatmaps. PHeatmaps is a program that offers users several functions: (1) to directly control the size of the cells, or text; (2) to automatically generate legends; (3) to annotate row and column; (4) to post-edit the heatmap; or (5) to separate clusters visually using spacers.
A Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner.
Supports visual data exploration. GENE-E is a matrix visualization and analysis platform that includes heat map, clustering, filtering, charting, marker selection, and many other tools. In addition to supporting generic matrices, it also contains tools that are designed specifically for genomics data. GENE-E is no longer supported, but can still be downloaded. It is now recommended to use new web-based tool, Morpheus.
A work space to graphically explore gene expression data. PermutMatrix uses the graphical Eisen approach, and extends it to optimal reorganization methods. It can also offer several methods for the optimal reorganization of rows and columns of a numerical dataset. This software yields different and complementary results than hierarchical clustering, therefore contributing to the understanding and identification of different gene expression profile. Large datasets can be thoroughly and quickly analyzed.
Allows to visualize gene or protein expression data in heatmaps. HemI linearly normalizes gene or protein expression data. It allows users to draw, manipulate and export publication-quality heatmaps in an user friendly manner. The tool can be used for experimentalists and bioinformaticians.
A package that provides rich functionalities for customizing heatmaps, arranging multiple parallel heatmaps and including user-defined annotation graphics. ComplexHeatmap reveals patterns and correlations among multiple sources of information with four real-world datasets.