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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.

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Documentation
Tool Name Tool Description Date Added
The Cancer Proteome Atlas
Proteomics

The Cancer Proteome Atals is a comprehensive bioinformatic resource for assessing, visualzing and analyzing the functional proteomics data of patient tumor and cell line samples.

 07/14/2017
The JBrowse Genome Browser
Visualization

JBrowse is a fast and scalable genome browser that runs on the web or as a desktop application. JBrowse supports a wide range of data types and genomic data formats, as well as over 50 software plugins to configure the appearance and behavior of the graphical interface.

 05/06/2019
The Laboratory for Individualized Breast Radiodensity Assessment (LIBRA)
Radiology Imaging

LIBRA is a fully-automatic breast density estimation software solution based on a published algorithm that works on either raw (i.e., “FOR PROCESSING”) or vendor post-processed (i.e., “FOR PRESENTATION”) digital mammography images. LIBRA has been applied to over 30,000 screening exams and is being increasingly utilized in larger studies.

 06/09/2017
Tools for neoantigen characterization and personalized cancer vaccine design (pVACtools)
Immuno-oncology

Neoantigens are tumor specific antigens arising from somatic mutations that can be targets for cancer immunotherapy. pVACtools enables identification, prioritization, and clinical application of neoantigens and supports all major sources of neoantigens and associated immunogenicity factors.

 08/18/2020
Tools for Quantitative Analysis of PET Imaging
Radiology Imaging

A collection of extensions for 3D Slicer to enable quantitative analysis of PET imaging data: image normalization, segmentation, and extraction of quantitative indices.

 07/14/2017
TOPAS
Radiation Research

Monte Carlo simulation of ionizing radiation transport for medical applications with focus on therapy and imaging with x-rays, electrons, protons and all other forms of ionizing radiation.

 01/03/2019
Trinity
Genomics, Transcriptomics

Trinity Cancer Transcriptome Analysis Toolkit (CTAT) including de novo transcriptome assembly with downstream support for expression analysis and focused analyses on cancer transcriptomes, incorporating mutation and fusion transcript discovery, and single cell analysis.

 06/09/2017
Tumor Heterogeneity Research Interactive Visualization Environment (THRIVE)
Pathology Imaging

A platform for quantitative evaluation of intratumoral spatial heterogeneity in multiplexed immunofluorescence images, via characterization of the spatial interactions between different cellular phenotypes and non-cellular constituents in the tumor microenvironment. A plugin mechanism enables researches to add and share their own heterogeneity algorithms.

 07/14/2017
TumorDecon
Transcriptomics

TumorDecon is an open source Python package that includes several deconvolution methods for estimating the relative abundance of cell types in a given tumor from its gene expression profile.

 08/19/2020
UCSC Xena
Analysis Platform, Genomics, Transcriptomics, Visualization

UCSC Xena securely analyzes and visualizes your private functional genomics data set in the context of public and shared genomic/phenotypic data sets such as TCGA, GDC, ICGC, TARGET, and the UCSC RNA-seq recompute compendium (TCGA + TARGET + GTEx).

 06/09/2017
WebMeV
Genomics

Web MeV (Multiple-experiment Viewer) is a web/cloud-based tool for genomic data analysis. Web MeV is being built to meet the challenge of exploring large public genomic data set with intuitive graphical interface providing access to state-of-the-art analytical tools.

 06/09/2017
XNAT
Radiology Imaging

XNAT is an open source imaging informatics platform designed to support institutional image repositories, image-based clinical trials, and translational imaging research.

 06/09/2017

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Questions or comments? Email us at nciitcr@mail.nih.gov.