To facilitate access to the latest bioinformatics tools and resources, the OSTR has developed license agreements with a variety of bioinformatics companies that provide software packages to analyze genomic and proteomic data. These tools are meant to be accessible to the majority of CCR investigators and NCI contractor employees engaged in collaborative arrangements with NCI investigators. NCI users can submit a request at https://service.cancer.gov under scientific software to gain access to these licenses. 

In addition training videos and tutorials are available for remote learning: 

Training Webinars & Tutorials

Scientific Software

Qlucore Omics Explorer

The CCR Office of Science and Technology Resources (OSTR) is pleased to announce the availability of institutional floating licenses of Qlucore Omics Explorer (QOE), including the NGS module, for the CCR community.  The QOE is an interactive data analysis and visualization software that enables biologists to find groups, structures, variable networks and discriminating variables in large Omics data sets, including public datasets.  Data types include gene expression data (NGS and arrays), DNA methylation, metabolomics, proteomics, etc.  QOE supports multiple visualization plots (e.g. 3D PCA, t-SNE, heat maps with hierarchical clustering etc.), a number of statistical methods (t-test, F-test (ANOVA), etc.) and an inbuilt Gene Set Enrichment Analysis (GSEA) workbench for pathway analysis.

Partek

Partek supports next generation sequencing (NGS), microarray, and qPCR data from all major vendors including Illumina, Thermo Fisher Scientific, Affymetrix, 10x Genomics, Dolomite Bio, Drop-Seq, Fluidigm, NanoString, Lexogen, Bio-Rad, Takara, and many others.

Ingenuity Pathway Analysis (IPA)

Leverage the largest source of expert-curated pathways content.

Genomatix Suite and the GGA/GMS platform for Next Generation Sequencing data analysis

Conducts a scientific analysis of genomic data, gene regulation, and expression generates and evaluates networks and pathways, performs extended literature searches and sequence analyses and extraction, visualizes our comprehensive genome annotation.

Geneious Prime

DNA, RNA, and protein sequence alignment, assembly and analysis software platform, integrating bioinformatic and molecular biology tools into a simple interface.

Clarivate Analytics/ MetaCore and MetaRodent

Integrated pathology pathways maps for disease mechanisms, gene-disease associations (putative biomarkers), and small molecule and biologics therapies, along with an extensive OMICS data repository.

CLC Genomics Server and CLC Genomics Workbench

Scalable computing solution for computationally demanding tasks like genome mapping and RNA-seq analysis.

Biodiscovery Nexus Software

Genetic aberration and expression analysis with an elegant and simple user interface.

SnapGene

SnapGene enables an easy and secure way to plan, visualize, and document everyday molecular biology procedures. With an intuitive interface, the software enables DNA sequence visualization, sequence annotation, sequence editing, cloning, protein visualization, and simulating common cloning methods. The software also enables documentation and sharing of data.

Lasergene

Lasergene Core Suite is a comprehensive DNA and protein sequence analysis software suite comprised of nine applications. Lasergene Core Suite is available in four configurations, each designed with different researchers in mind. This software includes functions for sequence assembly and SNP detection, automated virtual cloning and more.

Databases

Protein/Protein Interaction Database

Through a license agreement with Elsevier, the CCR community has access to the largest Y2H data set available in the world (CCR Database of Antibodies and Protein Interactions, C-DAPI). This dataset was derived from the same advanced Y2H screening methods utilized by Myriad Pharma’s ProNet program, which was used by many CCR laboratories to screen for binding partners to proteins of interest. The database contains over 120,000 non-redundant human protein interactions covering nearly one-half of the human genes in the NCBI RefSeq database.