TrioVis is a visualisation tool developed to assist filtering on coverage and variant frequency for genomic variants from exome sequencing of parent-child trios. It organises the variant data by grouping each variant based on the laws of Mendelian inheritance. Taking three Variant Call Format (VCF) files as input, the tool provides a user interface to test different coverage thresholds (i.e. different levels of stringency), to find the optimal threshold values, and to gain insights into the global effects of filtering.
ReadXplorer is a freely available comprehensive exploration and evaluation tool for NGS data. It extracts and adds quantity and quality measures to each alignment in order to classify the mapped reads. This classification is then taken into account for the different data views and all supported automatic analysis functions.
SAVoR is an easy-to-use web application that allows the user to visualize RNA-seq data and other genomic annotations on RNA secondary structures. SAVoR is designed to help researchers visualize sequencing data in the context of RNA secondary structures.
Clustergrammer is a web-based visualization tool with interactive features such as: zooming, panning, filtering, reordering, sharing, performing enrichment analysis, and providing dynamic gene annotations.
SNAVI (Signaling Networks Analysis and Visualization) is a Windows-based desktop application that implements standard network analysis methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means to visualize networks and network motifs. SNAVI is capable of generating linked web pages from network datasets loaded in text format. SNAVI can also create networks from lists of gene or protein names. SNAVI is a useful tool for analyzing, visualizing and sharing cell signaling data. SNAVI is open source free software.
DNA-Chip Analyzer (dChip) is a Windows software package for probe-level (e.g. Affymetrix platform) and high-level analysis of gene expression microarrays and SNP microarrays.
Gene expression or SNP data from various microarray platforms can also be analyzed by importing as external dataset. At the probe level, dChip can display and normalize the CEL files, and the model-based approach allows pooling information across multiple arrays and automatic probe selection to handle cross-hybridization and image contamination. High-level analysis in dChip includes comparing samples, hierarchical clustering, view expression and SNP data along chromosome, LOH and copy number analysis of SNP arrays, and linkage analysis. In these functions the gene information and sample information are correlated with the analysis results.
Started in Wing Wong Lab , Developed & Maintained by Cheng Li Lab.
VANESA is a software application for the visualization and analysis of biomedical networks in system biology applications to create systems that can answer fundamental questions and moreover, imitate cell behavior.