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 Website |
Code Repository |
Introductory Video |
Social Media |
Grant Info |
Documentation
| Tool Name | Tool Description | Date Added |
|---|---|---|
|
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 |
|
DICOM ToolKit (DCMTK) Radiology Imaging |
DCMTK is an open source DICOM toolkit. |
06/09/2017 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
Gene Set Enrichment Analysis (GSEA) and Molecular Signatures Database (MSigDB) Network Biology |
GSEA is software for identifying sets of genes representing the activation or dysregulation of biological processes or pathways in molecular data. GSEA can distinguish even subtle differences between phenotypes or cellular states and elucidate underlying mechanisms. The MSigDB is a companion resource of annotated gene sets for use with GSEA. |
07/30/2018 |
|
GenePattern Analysis Platform |
GenePattern is an analysis platform providing hundreds of tools for the analysis of multiple molecular data types. A web interface provides easy access to these tools and allows the creation of multi-step reproducible analysis pipelines. The GenePattern Notebook environment allows users to combine GenePattern analyses with Jupyter notebooks to create reproducible research narratives. |
06/09/2017 |
|
Globus Analysis Platform |
Cancer researchers use Globus for secure data transfer and sharing, task automation, and function execution, across distributed and heterogeneous environments at large scales. Tool developers integrate Globus services into data repositories and biomedical applications, leveraging Globus identity management, single-sign on, authorization, and search capabilities. |
04/05/2018 |
|
Gosling Genomics, Visualization |
Gosling is a grammar-based toolkit for scalable and interactive genomics data visualization. It allows creating a wide range of custom visualizations for genome-mapped data with unique interactive features, such as brushing, linking, and advanced zooming techniques. |
06/01/2021 |
|
HemOnc Ontology Medical Informatics |
OMOP-compatible ontology of anticancer regimens & supporting publications, with >95,000 concepts and >290,000 relationships. A portion is available through OHDSI: athena.ohdsi.org. The full ontology is freely available to academic and non-commercial users (CC-BY-NC-SA 4.0 license); a drug-focused subset is available to any user (CC-BY 4.0 license). |
07/13/2018 |
|
HistoQC Pathology Imaging |
HistoQC is an open-source tool which examines slides for artifacts and computes metrics associated with slide presentation characteristics (e.g., stain intensity, compression levels) helping to quantify ranges of acceptable characteristics for downstream algorithmic evaluation. |
09/09/2019 |
|
Integrated Methods for Predicting Enhancer Targets (IM-PET) Epigenetics, Genomics, Transcriptomics |
IM-PET is an open source software tool for identifying target genes of transcriptional enhancers. It uses four statistical features derived from transcriptomic, genomic, and epigenomic data. IM-PET is also available as a Docker container. |
07/25/2023 |
|
Integrative Genomics Robust iDentification of cancer subgroups (InGRiD) Genomics |
InGRiD (Integrative Genomics Robust iDentification of cancer subgroups) is a statistical approach to improve prediction of cancer subgroups and identification of key genes and pathways by integrating information from biological pathway databases. |
07/26/2018 |