Alternative splicing event visualization software tools | RNA sequencing data analysis
Alternative splicing is involved in many biological phenomena and has been better evidenced due to the development of next-generation sequencing (NGS) technologies. RNA-Seq technologies have facilitated the deep characterization of transcriptomes of several species. However, the huge amount of data generated in each experiment brings challenges for the analysis and interpretation of alternative splicing. This is particularly critical for researchers or research groups that lack bioinformatics expertise.
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.
Tests for differential usage of exons and hence of isoforms in RNA-seq samples. DEXSeq uses generalized linear models and offers reliable control of false discoveries by taking biological variation into account. It also detects with high sensitivity genes, and in many cases exons, that are subject to differential exon usage. DEXSeq achieves reliable control of false discovery rates by estimating variability for each exon or counting bin and good power by sharing dispersion estimation across features.
A quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer (IGV) or with a stand-alone command line program.
Detects, quantifies and displays differential splicing between groups of experiments. MAJIQ defines a general concept of local splicing variations (LSVs). It enables users to add previous transcriptome annotation with reliably-detected de-novo junctions from RNA-Seq experiments. This tool can capture all types of alternative splicing (AS) and many other variations which are more complex.
Enables visualization and navigation of reference genomes and corresponding genomic data sets. Savant is a genome browser that supports a wide range of file formats, as well as the use of remote files and datasources. Navigation to genomic regions of interest is assisted through textual search and bookmarks. The software delivers creative visualization representations for high-throughput sequencing (HTS) data and a plugin architecture that provides the opportunity to incorporate any computational tool within a visual environment.
A package to predict genes that are differentially spliced between two different conditions using RNA-seq data. This method allows users to detect tissue-specific alternative splicing in brain versus liver samples and tumour stage-specific alternative splicing in neuroblastoma patients. SplicingCompass reduces the number of statistical tests considerably and better accounts for combined effects..
Allows to display microarray data in their genomic context. EASAN is a user-friendly interface to genome-wide gene expression studies using microarrays and Next Generation Sequencing (NGS). This tool can (i) help biologists to rapidly and easily find relevant results from the latest technologies, (ii) enable gene expression regulation study at the gene level as well as at the exon level, and (iii) use different techniques as cited previously.