Bioinformatics
Bioinformatics services offered by the RIC cover a wide range of computational molecular biology applications, including genomics (DNA sequence variation), transcriptomics (gene expression), epigenomics (gene regulation), metagenomics (microbiome), metabolomics and lipidomics, and proteomics.
Supported analysis options include, but are not limited to:
Raw data QC and processing
- Quality control of raw FASTQ data
- Sample outlier detection
- Batch effect correction
- Genome or transcriptome alignment
Genomics
- Variant calling and annotation
- Genome assembly, including hybrid assemblies of long-read and short-read data sets
- Phylogenetic analysis
- Quality control and genotyping for Affymetrix Gene Titan arrays
Transcriptomics
- Gene or transcript quantification and differential analysis
- Cellular sub-population discovery for single-cell studies
- Quality control and normalization steps for microarray expression data
Epigenomics
- ChIP-seq, MEDIP-seq, and ATAC-seq peak calling and comparison
- Differential peak analysis
- Bisulfite sequencing methylation analysis
- Motif enrichment analysis and footprinting
Metagenomics
- Taxonomic identification and quantification for 16S amplicon sequencing
- Taxonomic and functional quantification for shotgun sequencing
- Metagenome or metatranscriptome assembly
- Diversity and differential analysis
Metabolomics
- Feature identification and quantification for metabolomics
- Differential analysis
Proteomics
- Protein identification
- Protein quantification and differential analysis in quantitative experiments
Statistics and machine learning
- Differential analysis
- Association analysis
- Clustering
- Dimensionality reduction techniques (PCA, NMDS, tSNE)
- Supervised machine learning
Systems biology
- Pathway enrichment analysis
- Molecular interaction networks
- Biomarker discovery and comparison
- Multi-omics data integration
Data visualization
- Heatmaps, box plots, scatterplots, and other types of plots
- Genome browsers/read pileups
- Custom visualizations
We offer collaborative, custom analysis solutions for any research project, and encourage researchers to consider collaborating with the RIC for all analysis stages of a project. We work with data from any facility, although we have a close relationship with the Sequencing Core (SQC), the Genomics Core (GMC), and the Mass Spectrometry Core (MSC), which provide excellent options for data collection at UIC.
In addition to support for any of the above types of analysis, the RIC also advises on experimental design, helping researchers optimize their use of biological replicates and sequencing depth; provides services like study design and randomization; creates custom visualizations of data, such as heat maps; and helps with manuscript preparation and grant applications.