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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.

Searching and Filtering Guidelines

Tool Name Tool Description Date Added
3D Slicer
Radiology Imaging

3D Slicer is the free open source software for medical image visualization and analysis.

06/09/2017
AMARETTO
Network Biology

AMARETTO for multi-omics data fusion and reformulations for pan-etiology and pan-cancer applications.

07/14/2017
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
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
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
ARCHS4
Transcriptomics

ARCHS4 provides gene and transcript counts uniformly processed from all the human and mouse RNA-seq samples from GEO.

08/11/2023
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
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
BioMuta
Genomics

Cancer associated gene mutation.

10/13/2017
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
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-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
CancerModels.Org
Models

CancerModels.Org is an open global research platform for patient-derived cancer models (PDCMs), including patient-derived xenografts, organoids, and cell line models. It is the largest open catalog of harmonized PDCMs and associated clinical, genomic, and functional data from academic and commercial providers. 

10/13/2017
cBioPortal for Cancer Genomics
Analysis Platform, Genomics, Transcriptomics, Visualization

The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. 

10/13/2017
Cistrome
Epigenetics

Curated and processed human/mouse ChIP/DNase-seq datasets in GEO, allowing users to search, browse, download ChIP-seq data signals, peaks, QC, motifs, target genes and similar datasets.

06/09/2017
Cistrome Explorer
Epigenetics

Cistrome Explorer is a powerful web-based visual analytics tool for exploring chromatin accessibility, histone modifications and transcription factor binding data across >200 samples. Compare patterns between cell types and conditions, and search Cistrome Data Browser for TFs bound near genes and in genomic intervals of interest.

08/18/2020
CLAMP-Cancer
Medical Informatics

A tool to quickly build customized natural language processing pipelines for extracting cancer information from pathology reports, though user-friendly interface with minimum programming knowledge.

07/14/2017
Clinical Interpretation of Variants in Cancer (CIViC) Knowledgebase
Variant Interpretation

CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer. Our goal is to enable precision medicine by providing an educational forum for dissemination of knowledge and active discussion of the clinical significance of cancer genome alterations.

06/09/2017
CNVnator/CNVpytor
Genomics

A tool for detection of somatic, subclonal, mosaic, and germline CNVs from sequencing.

07/30/2018
Cores Of Recurrent Events (CORE)
Genomics

CORE is a statistically supported computational method for finding recurrently targeted regions in massive collections of genomic intervals, such as those arising from DNA copy number analysis of single tumor cells or bulk tumor tissues.

06/09/2017

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