Core Facilities

Bioinformatics

In This Section

Core Facilities

General Information
Animal-Based Studies
Biochemical and Biophysical Studies
- Atomic Force Microscopy
- Biomolecular NMR
Biorepository
- Clinical Specimen Processing Core
- Institutional Biorepository
Cell-Based Studies
Multiomic Analysis
Informatics and Data Analysis
- Bioinformatics
- College of Medicine IT (Research Informatics)
Multiscale Imaging
Pathology and Specimen Processing Resources
Pharmacology
- Biomolecular NMR
- Drug Discovery, Development and Delivery
Research Software and Applications
- High-Performance Computing
Services

In collaboration with the Biomedical Research Core Facilities, Penn State Clinical and Translational Science Institute Biostatistics, Epidemiology and Research Design group (BERD) and the strategic plan team for Artificial Intelligence Informatics (BioAI), Penn State College of Medicine provides a variety of bioinformatics and biostatistics services, including analysis, prediction and software support.

Services available through the Genome Sciences Core and Mass Spectrometry and Proteomics Core are listed below and those offered through BERD can be found here.

Citation

Investigators using the Biomedical Core facilitates must cite the appropriate RRID and acknowledgement as written on the citation page of this website. Investigators using BERD should cite Penn State College of Medicine Bioinformatics and list the names of the software in the Materials and Methods section and the personnel services utilized in the Acknowledgements section of any article.

Instrumentation and Services

DNA Next Generation Sequencing (NGS) analysis
Exome-Sequencing analysis
ChIP-Seq analysis (narrow peaks or wider domains)
RNA-Seq analysis
DNA Methylation Sequencing analysis
Ribo-Seq analysis
Differential expression (RNA-Seq and DNA methylation)
Variant discovery (DNA and RNA-Seq)
Junction-based analysis of splicing events
ENCODE correlations with NGS datasets
The Cancer Genome Atlas (TCGA) NGS datasets
Epigenetic signature discovery
Transcription Factor Motif discovery
Phosphorylation prediction
microRNA target prediction
Virus de novo Assembly
Microarray analysis
Biomarker panel design
Pathway analysis
Gene ontology analysis
Proteomics analysis
qPCR analysis
Machine learning
Custom scripts/software
Single cell RNASeq data analysis
Genome wide association studies.
Metagenomic sequence data analysis.

Ingenuity Pathways
To obtain an IPA login with the University’s license, please call the Penn State Health Service Desk at 833-577-HELP (4357) and request access to the Ingenuity Pathway Analysis license. Currently, access is free, and the software may be accessed from any location with an internet connection.
MATLAB
MATLAB is available to all through the Penn State software portal for a nominal fee. A Mathworks License is free for students with some constraints.
Bioinformatics public software (bowtie, bwa, MACS, RSEG, Salmon, Kallisto, samtools, picard, IGV, GATK, GSEA, DAVID, hmmer, etc.)
R, Python, Perl, Java and other programming languages