Bio-Informatics Services

Data management and analysis services for investigators, researchers and collaborators

A scientist amidst DNA helixes working with a lab tube related to the Scripps Bio-Informatics Services.

Data management and analysis services for investigators, researchers and collaborators

The Scripps Health/Scripps Clinic Bio-Repository and Bio-Informatics Core provides data management and analysis services for Scripps Health and Scripps Clinic Medical Group investigators, as well as external researchers and collaborators. We offer scientific support to assist in the planning, collection, analysis, integration and dissemination of biomedical data and knowledge. Projects will often vary in time and cost depending on the scientific goals of the work, and the desired level of detail.

Our goal is to use existing software and tools developed by our group, along with open source software, to support science in a cost-effective manner. We have expertise in analyzing data and building tools across many different scientific areas.

Our main area of focus is Next-Generation Sequencing (NGS) and RNA Microarrays. Additionally, statistical data analysis on primary data and downstream functional analyses are available.

We offer the following services:

Experimental planning and optimization

  • Framing the clinical question(s) for conducting the experiment
  • Sample size planning, optimization and power calculations
  • Designing the ideal experimental setup to investigational methods
  • Design control and validation

NGS and microarray data analysis 

  • RNA-Seq and microRNA-Seq data analysis
  • ChIP-Seq data analysis
  • Custom bio-informatics workflows for NGS applications (RNA-Seq, ChIP-Seq, microRNA-Seq)
  • Gene expression analysis of in-house and published microarray datasets (e.g., Affymetrix, Illumina)
  • Quality control, alignment/mapping
  • de novo genome/transcriptome assembly (in the absence of a reference genome)
  • Integration and application of published and popular algorithms and tools
  • Multiple genome browser support for visualization of NGS results
  • Develop and integrate data analysis and visualization tools, including leveraging of R and other programming languages
  • Establishing and maintaining customized genomic databases
  • Statistical support and consultation including providing advice on various aspects of statistical design and analysis
  • Support grant applications with experimental design recommendations and power/sample analysis

Downstream analysis

  • Pathway and gene ontology analysis using publicly available tools (NIH DAVID, Panther, KEGG) as well as commercial software such as Partek Pathways and Ingenuity Pathway Analysis
  • Classification/Clustering analysis using R based pipelines for building prognostic and diagnostic classifiers
  • Preparation of research section and planning an analysis of research grants
  • Help with writing high quality manuscripts for peer-reviewed journals