OneStopRNAseq

OneStopRNAseq performs comprehensive processing and analysis of RNA sequencing (RNA-seq) data to provide data-quality control, differential gene expression, exon usage and alternative splicing analysis, transposable element expression analysis, allele-specific expression quantification, and gene set enrichment analysis.

Key Features:

• Versatile Analysis Workflows: Provides workflows for comprehensive data-quality control, differential gene expression, exon usage and alternative splicing, transposable element expression, allele-specific expression quantification, and gene set enrichment analysis.
• Data Input Flexibility: Accepts Gene Expression Omnibus (GEO) accession numbers or Dropbox links to sequence files, alignment files, gene-expression-count tables, or rank files together with corresponding metadata to integrate public and private RNA-seq datasets.
• Genome Build Specification: Supports specification of the genome build used for downstream analyses.

Scientific Applications:

• Genomics: Enables transcriptional analyses relevant to genomics research using RNA-seq datasets.
• Transcriptomics: Supports differential expression and transcript-level analyses for transcriptomic studies.
• Functional Genomics: Facilitates gene set enrichment and pathway analyses to interpret functional genomic results.
• Gene Regulation, Genetic Diversity, and Disease Mechanisms: Provides alternative splicing and allele-specific expression quantification applicable to studies of gene regulation, genetic variation, and disease mechanisms.

Methodology:

Automated bioinformatics pipelines integrate data-quality control, differential gene-expression analysis, exon usage and alternative splicing analysis, transposable element expression analysis, allele-specific expression quantification, and gene set enrichment analysis.