Tag Archives: Data Visualization

Analysis of large-scale omics data has become more and more challenging due to high dimensionality. More complex analysis methods and tools are required to handle such data. While many methods already exist, those methods often produce different results. To help ...

Advances in next-generation sequencing platforms have reshaped the landscape of functional genomic and epigenomic research as well as human genetics studies. Annotation of noncoding regions in the genome with genomic and epigenomic data has facilitated the generation of new, testable ...

Researchers from the Queensland Centre for Medical Genomics have developed PGTools, an open source software suite for analysis and visualization of proteogenomic data. PGTools is comprised of applications, libraries, customized databases and visualization tools for analysis of mass-spectrometry data using ...

Thanks to reduced cost of sequencing and library preparation, it is now possible to conduct a well-replicated RNA-Seq study for less than a few thousand dollars. However, if unforeseen problems arise, such as insufficient sequencing depth or batch effects, the ...

Strand specific RNAseq data is now more common in RNAseq projects. Visualizing RNAseq data has become an important matter in Analysis of sequencing data. The most widely used visualization tool is the UCSC genome browser that introduced the custom track ...

RNA-related applications of the next-generation sequencing (NGS) technologies require context-specific interpretations: e.g., sequence mismatches may indicate sites of RNA editing, or uneven read coverage often points to mature form of microRNA. Existing visualization tools traditionally show RNA molecules in two ...

Circleator is a Perl application that generates circular figures of genome-associated data. It leverages BioPerl to support standard annotation and sequence file formats and produces publication-quality SVG output. It is designed to be both flexible and easy to use. It ...

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. ...

Researchers from the Istituto per le Applicazoni del Calcolo, CNR, Italy, have developed RNASeqGUI R package, a graphical user interface (GUI) for the identification of differentially expressed genes across multiple biological conditions. This R package includes some well known RNA-Seq ...

Ultrahigh-throughput sequencing of cDNA (RNA-Seq) is an invaluable resource for investigating alternative splicing in an organism. Alternative splicing is a form of posttranscriptional regulation in which primary RNA transcripts from a single gene can be spliced in multiple ways leading ...