The Applied Bioinformatics Core (ABC) is a central service group specializing in providing data management and analysis support to large genomic centers and research groups. ABC has expertise in analyzing biological data from diverse types of experiments, including high- throughput genomic assays, single cell experiments and spatial profiling platforms. The core has extensive experience building standardized workflows and customized, in-depth analyses, visualization and functional interpretation with emphasis on quality control and statistical rigor. ABC performs detailed computational analyses driven by specific biological questions defined by investigators and provides extensive reports with publication-ready images and the analysis source code.
Core Technologies/Services
Single Cell and Spatial Genomics Analyses
- Single cell transcriptomics
- Single cell ATAC
- Single cell methylation
- Single cell TCR/BCR profiling
- Multimodal single cell studies
- Spatial transcriptomics
Transcriptomics
- Differential gene expression analysis
- General RNA biology assays such as CLIP-seq or PRO-seq
Epigenetics Analyses
- ChIP-seq
- ATAC-seq
- Reduced representation bisulfite sequencing (RRBS) or targeted methylation
- Whole Genome Bisulfite sequencing
Genomics
- Variant calling and annotation
- Evolution of viral sequences
- Classifications of pathogens
Computational Pipelines
- Large scale automation of analysis pipelines
- Distribution and management of large datasets
- Shiny apps for data visualization and analysis
Training and Consulting
- Experimental design
- Weekly walk-in clinic hour
- Hands-on workshops
- Programing advice and code sharing