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A Penn State Nittany Lion statue is seen in the courtyard of Penn State College of Medicine in Summer 2016. The statue is in focus toward the right side of the image. Out of focus in the background, green plants and trees are visible in the courtyard.

Bioinformatics

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.

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Instrumentation and Services

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  • 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.
Software Support Expand answer
  • 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

Procedures, Protocols and Forms

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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.

Work With Bioinformatics

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