The Bioinformatics Core Facility at UPMC Children's Hospital of Pittsburgh (BCF@CHP) is a resource to support the bioinformatics analysis needs of investigators for datasets generated by the Sequencing Core at Rangos (HSSC@CHP ), by outside sequencing resources, or by using publicly available datasets.
The Core helps investigators in building standardized workflows as well as customized, in-depth analyses with emphasis on quality control and statistical rigor. The services listed below should give you an impression of the most commonly performed analyses - we are by no means limited to them and are happy to tackle new challenges. We can provide extensive reports with publication-ready images as well as the analysis source code upon request. If you come across a paper with sequencing data analyses or other statistical methodology you would like to use (or think the Core should be aware of), please email it our way!
NGS data analysis
|GENOMICS (WGS, WES)||EPIGENOMICS (CHIP-seq, ATAC-seq)|
|TRANSCRIPTOMICS (Arrays, RNAseq)||OTHER ANALYSIS|
- Supervised machine learning approaches for classification purposes, and feature prediction
- Establish novel analysis pipelines using multivariate-, multiblock-, and network-based analysis for systems-level integration of -omics data across platforms
- Data visualization including heatmaps, violin plots, and other types of plots as well as custom visualizations
- Automation of analysis pipelines using Nextflow
- Literate programming using Rmarkdown
Planning a data-intensive project? We are available for long-term collaborations on projects that require a higher level of analysis or the development of custom analysis pipelines. We can also co-mentor students who are interested in performing their own analysis or developing their own methods.
The BCF@CHP is dedicated to supporting grant applications for researchers at Rangos Research Center, and other external users. In addition to Letters of Support detailing Core capabilities as they relate to a proposed project, we can also assist with crafting the study design and research strategy, and devising the budget for informatics analysis. Please also consider including a member of the Core as a Co-Investigator in your application, which can strengthen your application by showing the collaborative involvement and support of an informatics expert.
If you expect to use particular Bioinformatics services to carry out your research project and would like our assistance with your application, please contact us. Please note that the time necessary to develop this plan may vary based on the complexity of your project.
To request a Letter of Support, please email firstname.lastname@example.org with the following details:
- PI first and last name
- Requestor name, if not PI
- Draft letter, including your project title and a brief description of the proposed impact of the work.
- Specific aims (a draft copy is fine)
- Name of funding agency
- Any additional details about your project or other services
Although not currently deployed, we will be developing training events/workshops to enable researchers to do their own analysis.
ACKNOWLEDGING CORE SUPPORT
Please acknowledge Core staff where appropriate and consider authorship inclusion when scientific contributions merit. In cases, where extensive bioinformatics analyses have been customized for your research project, we can assist with manuscript preparation, and preparation of figures. Please find more details at the School of Medicine's Authorship policy
CONTACT AND DIRECTIONS
Mailing address: Rangos Research Center Rm. 8132
UPMC Children's Hospital of Pittsburgh
4401 Penn Avenue .
Pittsburgh PA 15224