Tag Archives: Sequence Read Archive

The Sequence Read Archive (SRA) contains over one million publicly available sequencing runs from various studies using a variety of sequencing library strategies. These data inherently contain information about underlying genomic sequence variants which...

RNA-Seq Viewer is a web application that enables users to visualize genome-wide expression data from NCBI’s Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. The application prototype was created by a small team during a three-day hackathon facilitated ...

Pulmonary Fibrosis News – by Pais Teresa – Researchers have identified 39 genes as critical to idiopathic pulmonary fibrosis (IPF), based on a computational analysis of large genomic studies. Their study, “Detecting the Molecular System Signatures of Idiopathic Pulmonary Fibrosis through Integrated Genomic ...

Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0. Researchers ...

recount is a resource of processed and summarized expression data spanning nearly 60,000 human RNA-seq samples from the Sequence Read Archive (SRA). The associated recount Bioconductor package provides a convenient API for querying, downloading, and analyzing the data. Each processed ...

The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control) to very complicated (e.g., time series involving multiple samples at each time point with separate drug treatments). Most ...