Tools and Resources

Bioinformatics is familiar with all of these resources and we are happy to help investigators leverage them in their research. 

BBSR-developed Tools

Bioinformatics is developing several tools to empower and encourage investigators to analyze their own data. The tools are developed so that no specific coding or bioinformatics experience is necessary. Here are some of our tools:

RNA-seq analysis 

• This analysis platform allows investigators to perform many types of analysis downstream of RNA-seq data. To access the app, the core will have to upload the processed data in the form of raw counts. 
• If you don't have access yet, you can access the tool with the tutorial available here.

Analysis from differential expression data

• This analysis platform allows investigators to explore differential expression and pathway analysis. The input is any table of differential gene expression and can come from either RNA-seq or microarray data. An advantage of this platform is that investigators can use any processed differential expression data without the direct assistance of the core. 

Upregulator and pathway analysis from gene list input

• In this platform, investigators can input a list of interesting genes and perform transcriptional regulator and pathway analysis. An advantage of this platform is that genes that are selected from any starting material can be inputted and analyzed. 

Other tools in development

Actively developed tools include functional screen analysis, single-cell RNA-seq analysis, and CyTOF analysis.

Access to these tools is free if the data is suitable. Contact us to discuss your data and to determine if it is already in the correct format. 

Licensed Software

Oncomine

Oncomine Research Edition is a powerful web application that integrates and unifies high-throughput cancer profiling data so that target expression across a large volume of cancer types, subtypes and experiments can be assessed online, in seconds. 

The program offers an initial login for free. University of Colorado Cancer Center members should register and work with the free version until they become familiar with the program. When members are ready to finalize their analyses, they can contact Core manager Andrew Goodspeed and he will set them up with an upgraded login. Please logout every time you finish an analysis. 

Members should understand that the University of Colorado Cancer Center only has two upgraded versions and that they are shared. All logins should be used and relinquished as quickly as possible.

Ingenuity Pathway Analysis (IPA)

A commercial pathway analysis tool that can be accessed by contacting the Genomics Shared Resource. The BBSR also has a license on a remote computer. Contact Andrew Goodspeed if interested. 

Public Datasets & Collections

Large Pharmacogenomics Datasets

Cancer Cell Line Encyclopedia (CCLE)

Genomics of Drug Sensitivity in Cancer (GDSC)

Cancer Therapeutics Response Portal (CTRP)

Dataset Collections

BioPortal

Genomics Data Commons

Gene Expression Omnibus (GEO) 

We can also assist in gaining access to controlled use data (ex. dbGap) by helping with and being included on access applications.

Public Tools & Resources

Morpheus (Make heatmaps)

Gene set enrichment analysis (GSEA) (Pathway analysis) 

DAVID (Pathway analysis)