We maintain a wide variety of bioinformatics software above and beyond what is provided in R, Python and most widely used academically developed tools. We use Gitlab a project management tool and Github to share our resources. We maintain Galaxy as a web-based platform for biomedical data analysis. Our tool box includes but is not limited to the software listed below.
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.
SeuratViewer reads in the expression data, sample data, feature annotation, dimensionality reduction/ clustering, and marker gene information as an RData object and enables users to view and interact with their single cell RNAseq data
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.
Vector NTI® Advance
Vector NTI® Advance software is the most highly integrated, multifunctional desktop sequence analysis application suite available today and provides superior integration, data management, and scalability.
TRANSFAC provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes.