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 Website |
Code Repository |
Introductory Video |
Social Media |
Grant Info |
Documentation
| Tool Name | Tool Description | Date Added |
|---|---|---|
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 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 Cancer Imaging Archive (TCIA) Radiology Imaging |
TCIA is NCI’s repository for publicly shared cancer imaging data. TCIA collections include radiology and pathology images, clinical and clinical trial data, image derived annotations and quantitative features and a growing collection of related ‘omics data both from clinical and pre-clinical studies. |
10/13/2017 |
|
The Cancer Dependency Map Portal Analysis Platform, Visualization |
The DepMap Portal empowers researchers to make discoveries related to cancer vulnerabilities by providing open access to key datasets, analytical tools, and visualizations. |
06/03/2021 |
|
Texomer Transcriptomics |
Texomer deconvolutes allele-specific copy number and mRNA expression levels from paired exome and transcriptome sequencing data of tumor tissue samples and outputs variants associated with tumor specific transcriptional regulation. |
06/09/2021 |
|
spatialGE web application Transcriptomics |
spatialGE is a user friendly, point-and-click, web application that facilitates spatial transcriptomics data analysis. This application contains a collection of analytical methods for visualization and statistical analysis of the tissue microenvironment. Users can create accounts to manage their data and projects, as well as generate figures and tables to report results. |
09/10/2023 |
|
spatialGE R package Transcriptomics |
spatialGE R package is an analytical suite for the visualization and spatial statistics analysis of spatially-resolved transcriptomics data. The spatialGE R package features a data object to store data and results from multiple tissue sections, as well as associated methods to detect spatial patterns in the expression of individual genes and gene sets. |
09/10/2023 |
|
SlicerDMRI Radiology Imaging |
Diffusion magnetic resonance imaging for neurosurgical planning in 3D Slicer open-source software. |
06/09/2017 |
|
Single Cell Genome Viewer (SCGV) Genomics |
Graphics user interface for single-cell genomics. |
07/07/2017 |
|
SampleMap Genomics |
Projects samples into a GoogleMap explorer to allow overlaying omics attributes to spot patterns quickly. A TumorMap version was built for TCGA analysis. |
06/09/2017 |