Tag: Visualization

SuperTranscripts

[PMID: 28778180] [Genome Biology]

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

“Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a single sequence. The Lace software is provided to construct superTranscripts from any set of transcripts, including de novo assemblies. “

SVPV

[] [Bioinformatics]

SVPV: A Structural Variant Prediction Viewer for paired-end sequencing datasets

“a tool which presents a visual summary of the most relevant features for SV prediction from WGS data. SV calls from multiple prediction algorithms may be visualised together, along with annotation of population allele frequencies from reference SV datasets. Gene annotations may also be included. The application is capable of running in a GUI mode for visualising SVs one by one, or in batch mode for processing many SVs serially.”

Ark

[PMID:28003258] [Bioinformatics]

The Ark: a customizable web-based data management tool for health and medical research

“The system provides data management for core research information including demographic, phenotype, biospecimen and pedigree data, in addition to supporting typical investigator requirements such as tracking participant consent and correspondence, whilst also being able to generate custom data exports and reports.” It could be a good alternative to Progeny.

JunctionSeq

[PMID:27257077] [Nucleic Acids Research]

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq

JunctionSeq is capable of detecting differential usage of 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.”