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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          |
Social Media          |
Grant Info          |
Documentation
Tool Name Tool Description Date Added
Gaussian Mixture Model and Proportion Test (GMAP)
Genomics

The spatial organization of the genome plays a critical role in regulating gene expression. GMAP is an open source software tool for modeling 3-dimensional chromosomal domains using Hi-C data. GMAP is also available as a Docker container.

 05/20/2019
GARDE
Medical Informatics

GARDE is a clinical decision support platform that (i) executes algorithms on electronic health record data compliant with the FHIR standard to identify patients who meet genetic testing criteria for hereditary cancer; and (ii) uses a scripted chatbot to provide patients with education and access to genetic testing.

 07/19/2018
Galaxy-P multi-omics
Analysis Platform, Proteomics

A unified platform for integrative genomic-proteomic-metabolomic data analysis and informatics in cancer research.

 06/09/2017
Galaxy
Analysis Platform

Galaxy is a Web-based computational workbench that anyone can use to analyze large biomedical datasets. There are >9500 software tools and visualizations integrated into Galaxy for analysis of single-cell and bulk omics, live cell and molecular imaging, machine learning, microbiome, and much more. Galaxy also includes many ITCR tools and visualizations.

 10/01/2019
Federated Tumor Segmentation (FeTS)
Radiology Imaging

FeTS is an open-source toolkit with a user-friendly graphical user interface, that aims to i) bring pre-trained segmentation models closer to clinical experts and researchers, and ii) allow secure multi-institutional collaborations via federated learning to improve these pre-trained models without sharing patient data, thereby overcoming legal, privacy, and data-ownership challenges.

 12/02/2021
FaNDOM
Genomics

FaNDOM is a fast and open source method for aligning Bionano Saphyr optical map molecules and contigs to a reference, with the goal of identifying structural variation in genomes. FaNDOM utilizes a seed-based filter to speed up the searches. FaNDOM is implemented in C++ and supports multithreading.

 12/13/2021
Enhancer Linking by Methylation/Expression Relationships (ELMER)
Epigenetics

R tool for analysis of DNA methylation and expression datasets. Integrative analysis allows reconstruction of in vivo transcription factor networks altered in cancer along with identification of the underlying gene regulatory sequences.

 06/09/2017
Electronic Medical Record Search Engine (EMERSE)
Medical Informatics

EMERSE is powerful, enterprise-grade, search and text processing software for unstructured electronic health record documents. It can be used for a variety of clinical research tasks including cohort identification, eligibility determination, and general data abstraction. EMERSE has been implemented at academical medical centers nationwide.

 07/19/2018
ecSeg
Genomics

This repository is the official version of ecSeg, a tool used to quantify ecDNA in DAPI-stained images. It also has an extension to analyze FISH probes.

 12/31/2021
DINC 2.0
Protein Structure

DINC 2.0 is a parallelized meta-docking method for the incremental docking of large ligands (currently using AutoDock Vina).

 07/14/2017
DICOM ToolKit (DCMTK)
Radiology Imaging

DCMTK is an open source DICOM toolkit.

 06/09/2017
DANA
Transcriptomics

DANA (DAta-driven Normalization Assessment) guides the selection of a depth normalization method in a microRNA sequencing data set, using biology-motivated and data-driven metrics. For each method, its metrics allows assessment of (1) how effectively normalization removes handling effects and (2) how normalization biases true biological signals.

 12/02/2021
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
CNVnator/CNVpytor
Genomics

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

 07/30/2018
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
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
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
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
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
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

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