The ITCR Program funds informatics tools that support data across the cancer research continuum. All of the tools are free for use by academic and non-profit researchers. Access to tools, code repositories and introductory videos is available through the links in the table below.
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Tool Name | Tool Description | Date Added |
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Cancer-Related Analysis of Variants Toolkit (CRAVAT) Variant Interpretation |
OpenCRAVAT is a biologist-friendly software platform of annotation, visualization, and analysis tools to interpret cancer mutations. It includes an app store with 150+ tools, a pipeline-friendly command line interface, and an interactive, richly detailed graphical interface. It is available on the web, cloud, and for secure local installation. |
06/09/2017 |
Cancer Slide Digital Archive (CDSA) Pathology Imaging |
The CDSA is a web-based platform to support the sharing, managment and analysis of digital pathology data. The Emory Instance currently hosts over 23,000 images from The Cancer Genome Atlas, and the software is being developed within the ITCR grant to be deployable as a digital pathology platform for other labs and Cancer Institutes. |
06/09/2017 |
Cancer Imaging Phenomics Toolkit (CaPTk) Radiology Imaging |
Quantitative image analysis package offering radiomic features and machine learning signatures for oncologic images, as well as predictive tools especially for breast and brain cancer. Both command-line and UI-based versions. CapTk is distributed under a BSD-style license. |
06/09/2017 |
BioMuta Genomics |
Cancer associated gene mutation. |
10/13/2017 |
Bioconductor Analysis Platform |
The Bioconductor project offers over 2,000 open-source software and data packages and is essential to modern cancer genomics research. ITCR supports key infrastructure benefiting thousands of researchers from academia, government, and industry who use and develop Bioconductor tools, furthering our knowledge and treatment approaches for cancer. |
06/09/2017 |
Averon Notebook Proteomics |
Averon Notebook provides a computational environment to identify new therapeutically actionable mechanisms of oncogenic signaling enabled by mutant-directed protein-protein interactions to inform target discovery in cancer. |
09/16/2023 |
ARCHS4 Transcriptomics |
ARCHS4 provides gene and transcript counts uniformly processed from all the human and mouse RNA-seq samples from GEO. |
08/11/2023 |
Apache Clinical Text and Knowledge Extration System (cTAKES) and Cancer Deep Phenotype (DeepPhe) Medical Informatics |
Deep Phenotyping for Cancer (DeepPhe) uses natural language processing (extending the Apache clinical Text Analysis and Knowledge Extraction System [cTAKES] platform), visual analytics, and ontology-based summarization to extract cancer-specific information from electronic medical records. A range of output formats and API access are provided. |
06/09/2017 |
AmpliconReconstructor (AR) Genomics |
Reconstructs complex variation and disambiguates Amplicon Architect based reconstructions using BioNano optical mapping data and an NGS-derived breakpoint graph. |
12/13/2021 |
AmpliconArchitect (AA) Genomics |
AmpliconArchitect (AA) is a tool which can reconstruct the structure of focally amplified regions in a cancer sample using whole genome sequence short paired-end data. A full description of the methods and detailed characterization of copy number amplifications and ecDNA in cancer can be found in the following manuscript. |
12/13/2021 |
AMARETTO Network Biology |
AMARETTO for multi-omics data fusion and reformulations for pan-etiology and pan-cancer applications. |
07/14/2017 |
3D Slicer Radiology Imaging |
3D Slicer is the free open source software for medical image visualization and analysis. |
06/09/2017 |