Gene fusion visualization software tools | RNA sequencing data analysis
The discovery of novel gene fusions in tumor samples has rapidly accelerated with the rise of next-generation sequencing. A growing number of tools enable discovery of gene fusions from RNA-seq data. However it is likely that not all gene fusions are driving tumors. Assessing the potential functional consequences of a fusion is critical to understand their driver role. It is also challenging as gene fusions are described by chromosomal breakpoint coordinates that need to be translated into an actual amino acid fusion sequence and predicted domain architecture of the fusion proteins.
Enables users to explore large, integrated genomic datasets. IGV provides next-generation sequencing (NGS) data visualization and provides features for identification of sequencing and analysis artifacts, leading to errant single-nucleotide variant (SNV) calls, as well as support for viewing large-scale structural variants (SV) detected by paired-end read technology. The software also includes features to support third-generation long-read sequencing technologies. Several IGV features have been developed to aid manual review of aligned reads.
Provides multiple tools for visualizing chimeric RNA molecules as well as functions for sorting and filtering candidates. Chimeraviz is a Bioconductor package that visualizes chimeric RNA and implements a unified format for representing fusion transcripts. This package can take input from multiple fusion-finder tools. These functionalities could facilitate the prioritization of true positive and important fusion transcripts.
Deduces the molecular interactions and pathways associated with a fusion. FusionPathway also serves for the investigation of potential therapeutic targets in these pathways. It can assist researchers for developing therapeutic strategies for patients who harbor undruggable fusions. This tool enables the prediction of novel molecular interactions of proteins on the basis of multiple domain combinations.
Creates multiple visualizations for annotating each gene fusion, at the transcript- and protein-level. INTEGRATE-Vis evaluates gene expression within an individual sample or across a cohort. It can be used to construct domain plot to translate the fusion transcript and can display the corresponding protein domains. This tool is able to show the ranges of read coverage for each gene partner in an automatically way.
Performs alignments to fusion and non-fusion gene constructs simultaneously. FuSpot locally aligns and maps reads against fusion reference sequences to allow users to visualize and pinpoint fusion breakpoint evidence. The software enables researchers to critically inspect candidate fusion breakpoints derived from ribonucleic acid (RNA) fusion detector tools. It permits the identification and elimination of obvious false positives and to systematically select candidates for downstream validation. Besides, it can facilitate gene fusion studies that can lead to more targeted cancer therapies.
Allows visualization of detected gene fusions on the transcript level. TViewer provides functions for visually integrating transcript annotations and gene fusions with RNA-seq data. It enables medical researchers to utilize a robust and comprehensive platform for detecting, visualizing and interpreting gene fusions. This tool interactively inspects transcript fusion expression from Gene Fusion analyses.
Allows users to perform on different subjects: alignment steps, quality control (QC), differential gene expression and pathway analyzes. VIPER utilizes a computational workflow management system named Snakemake to combine many tools currently employed in RNA-seq analysis. Moreover, it includes a variety of optional steps for variant analysis, fusion gene detection, viral DNA detection and evaluation of potential immune cell infiltrates.
Allows users to explore fusion genes discovered in RNA-seq data. Clinker allows raw reads involved in the discovery of fusion genes to be viewed and inspected in IGV. It generates annotations of transcripts and protein domains. It uses a transcriptome reference (superTranscripts) containing only the transcribed sequence of a gene and providing compact reference for analysis and visualization of RNA-Seq. It is useful for visualizing fusion genes and studying details.
A python package to annotate and visualize gene fusions. For a given gene fusion, AGFusion will predict the cDNA, CDS, and protein sequences resulting from fusion of all combinations of transcripts and save them to fasta files. AGFusion can also plot the protein domain architecture of the fusion transcripts.
Provides a visualization tool for gene fusion. FusionView is a web application that provides circular view, domain architecture view and network view. The circular view takes gene pairs in headgen-tailgen format and allows batch visualization. The domain view displays all known fusion breakpoint locations, exonic structures and proteins domains. Finally, the gene fusion network suits for exploring fusion partnerships.
Allows exploration of fusion gene. iFuse performs a comparison of two or more genomes. It permits users to visualize all detected structural variation (SV) events and fusion genes determined in their results and provide the concomitant candidate transcripts and polypeptide sequences associated with the detected fusion genes. This tool can also categorize and filter structural variation analysis.
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