Genome Studio is a tool to visualize and analyze data generated on Illumina array platforms, which supports the primary analysis of microarray data.
Ingenuity Pathway Analysis (IPA)
IPA is an all-in-one, web-based software application that enables analysis, integration, and understanding of data from gene expression, miRNA, and SNP microarrays, as well as metabolomics, proteomics, and RNAseq experiments.
Core staff are proficient with the use of the R statistical programming software package. This is a freely available and powerful software package that has a wide range of analysis tools for computational and statistical analysis.
TRANSFAC provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes.
Tree-Based Pipeline Optimization Tool (TPOT)
TPOT is a software package developed by the Computational Genetics Laboratory at Penn for automated machine learning (AutoML). TPOT is available as open-source.