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IGV / Integrative Genomics Viewer
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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.
ALEXA-Seq
Analyzes parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues. ALEXA-Seq comprises several functions: (1) creation of a database of expression and alternative expression sequence ‘features’, (2) mapping of short paired-end sequence reads to these features, (3) identification of features that are expressed above background noise while taking into account locus-by-locus noise, or (4) identification of features that are differentially expressed in samples.
Savant
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.
DEXSeq
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.
AVISPA / Advanced Visualization of Splicing Prediction and Analysis
Splices prediction and analysis. AVISPA predicts whether the exon is alternatively spliced, displays tissue-dependent splicing patterns, and whether it has associated regulatory elements. The tool offers an in silico analysis of regulatory features and the mapping of putative regulatory sequence motifs in the genome. The prediction technique is based on a Bayesian neural network, which provides improved prediction accuracy compared to a battery of other methods.
JunctionSeq
An R/Bioconductor package that builds on the statistical techniques used by the well-established DEXSeq package to detect differential usage of both exonic regions and splice junctions. In particular, JunctionSeq is capable of detecting differentials in novel splice junctions without the need for an additional isoform assembly step, greatly improving performance when the available transcript annotation is flawed or incomplete. JunctionSeq also provides a powerful and streamlined visualization toolset that allows bioinformaticians to quickly and intuitively interpret their results.
SplicePlot
A package for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. SplicePlot takes mapped RNA sequencing reads and genotype data as input and outputs publication-quality Sashimi plots, hive plots and structure plots, enabling better investigation and understanding of the role of genetics on alternative splicing and transcript structure. Such visualizations take advantage of the high precision quantification of RNA-seq and enable a better understanding of the genetic effects behind alternative splicing in RNA-seq data.
MAJIQ / Modeling Alternative Junction Inclusion Quantification
Provides a method to detect, quantify and visualize differential splicing between groups of experiments. Two key features distinguish MAJIQ from other algorithms. First, MAJIQ does not quantify whole gene isoforms. Instead, MAJIQ defines a more general concept of “local splicing variations”, or LSVs. Briefly, LSVs are defined as splits in a gene splice graph where a reference exon is spliced together with other segments downstream (single source LSV) or upstream of it (single target LSV). The second important distinguishing element of MAJIQ is that it allows users to supplement previous transcriptome annotation with reliably-detected de-novo junctions from RNA-Seq experiments.
EASANA
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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.
Cascade
Allows displaying and explores next generation sequencing (NGS) datasets in a rapid and intuitive way by permitting multiple data attributes to be shown simultaneously. Cascade can analyze RNA-seq data, or whole-exome or genome sequencing (WES/WGS). It employs a variety of tunable parameters to highlight specific attributes of genes/features that are of interest to the researcher. This tool allows researchers and clinicians to make transition from data exploration to hypothesis generation.
dSpliceType
A generalized framework to systematically investigate the synergistic and antagonistic effects of differential splicing and differential expression. dSpliceType detects and prioritizes a list of genes that are differentially expressed and/or spliced. In particular, the multivariate dSpliceType is among the fist to utilize sequential dependency of normalized base-wise read coverage signals and capture biological variability among replicates using a multivariate statistical model.
Splicing Express
Provides a simple and effective way for the identification, annotation and visualization of Alternative Splicing Events (ASEs). Splicing Express is a software suite that provides expression graphics in an intuitive fashion. It is able to extract meaningful information from deep transcriptome data and performs statistical analysis aiming to give significance values to the fold differences between the splicing variants. The complete automation in Splicing Express makes it a useful tool for deep analysis of ASE in any transcriptome.
ViennaNGS
An integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. ViennaNGS comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.
WASP / Website for Alternative Splicing Prediction
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Combines subgroups of features into a network, allows different tissues to share feature subgroups. WASP uses hidden variables within a network architecture to model non-linear relationships between putative regulatory features and splicing changes. It can be applied to datasets profiling larger numbers of tissues, different species, and different types of alternative splicing. The tool was tested and achieves relative improvements of 52% in splicing code quality and up to 22% in classification error, compared with the state of the art.
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