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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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Tool Website          |
Code Repository          |
Introductory Video          |
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Grant Info          |
Documentation
Tool Name Tool Description Date Added
OpenChallenges
Analysis Platform

OpenChallenges.io is a centralized hub for biomedical challenges that empowers participants with the most up-to-date information about relevant challenges, while providing organizers with standardized challenge event templates and intelligence.

 08/29/2023
OpenInfobutton
Medical Informatics

Open source suite of Web services that enables integration of online clinical evidence resources with Electronic Health Record (EHR) systems using the Health Level Seven (HL7) Infobutton Standard. We are extending the OpenInfobutton suite to include automatic summarization of clinical evidence resources for cancer prevention.

 07/19/2018
OpenStats
Models

A Bioconductor R package with several statistical methods for identifying genotype to phenotype associations. Developed by the International Mouse Phenotyping Consortium (https://www.mousephenotype.org/ ) for high-throughput pipelines, with an emphasis on managing temporal variation, and adaptable for PDX mouse strain analysis.

 06/09/2017
Overture
Analysis Platform

Overture is a collection of modular, open-source software components designed to make the management of big-data genomic projects both easy and more cost effective. The Overture system promotes FAIR data sharing of genomic datasets by overcoming the major obstacles in storing, managing, exploring, and distributing massive genome-scale datasets.

 08/29/2023
Pathology Imaging Informatics Platform (PIIP)
Pathology Imaging

Freely downloadable pathology viewer which supports viewing, annotation and analysis of Whole Slide Images. Functionality will be extended as part of the Pathology Image Informatics Platform.

 06/09/2017
Personalized Cancer Therapy
Genomics, Medical Informatics

Curated website cataloguing clinically actionable information for personalized cancer therapy including clinically significant genetic variants and drug-gene association.

 06/09/2017
PRECISION.seq
Transcriptomics

PRECISION.seq enables an objective and systemic evaluation of depth normalization methods for microRNA sequencing, in the context of differential expression analysis, using realistically distributed and robustly benchmarked data. Users can assess their chosen methods and compare their performance to nine methods already implemented in the package.

 12/02/2021
QIIME 2
Analysis Platform

QIIME 2 is an end-to-end microbiome data science platform that is widely used for investigation of the human microbiome, including diverse research across the cancer research continuum. QIIME 2 was designed to ensure reproducible bioinformatics and to facilitate accessibility by users with varying degrees of computational sophistication.

 08/14/2020
Quantitative Image Informatics for Cancer Research (QIICR) Tools Catalog
Radiology Imaging

A collection of tools to promote the adoption of quantitative imaging tools and DICOM standard in medical imaging research.

 02/06/2018
Quantitative Imaging In Pathology (QUIP)
Pathology Imaging

Quantitative Imaging in Pathology (QuIP) is a digital microscopy software platform for cancer research. It consists of microservices and web applications that support viewing, annotation, and data management of whole slide tissue images and Pathomics image analyses.

 06/09/2017
RADIOMICS.io
Radiology Imaging

RADIOMICS.io is an open-source platform for informatics developments for radiographic phenotyping using automated engineered and deep learning technologies. With this platform, we aim to establish a reference standard for radiomic analyses, provide a tested and maintained resource, and grow the radiomic developers' community.

 06/09/2017
RadxTools
Radiology Imaging

RadxTools is a new image informatics toolkit specifically geared towards developing modules that enable (a) creation of spatially aligned deeply-annotated radiology-pathology datasets, (b) quantitative characterization of specialized tumor response-specific features on post-treatment imaging, and (c) quality control of radiomic features.

 06/03/2021
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
Single Cell Genome Viewer (SCGV)
Genomics

Graphics user interface for single-cell genomics.

 07/07/2017
SlicerDMRI
Radiology Imaging

Diffusion magnetic resonance imaging for neurosurgical planning in 3D Slicer open-source software.

 06/09/2017
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
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
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
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
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

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