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 |
|---|---|---|
|
mCodeGPT Medical Informatics |
This Python package harnesses the power of large language models like GPT-4 to automatically extract entities from raw text associated with a given cancer ontologies and Knowledge Bases. Input research text and mCodeGPT will output structured data in tabular format. |
09/10/2023 |
|
Lisa: Epigenetic Landscape In Silico deletion Analysis Epigenetics, Transcriptomics |
Lisa is a web-based tool and Python software package for predicting transcriptional regulators of differentially expressed gene sets. Lisa combines histone modification ChIP-seq and chromatin accessibility profiles to identify cis-regulatory regions, and uses transcription factor ChIP-seq to determine relevant regulatory transcription factors. |
07/26/2023 |
|
LesionTracker / OHIF Web Image Viewer Radiology Imaging |
Extensible open-source zero-footprint web image viewer for oncology imaging. "LesionTracker" is a web browser based platform for viewing and measuring lesion metrics for tracking oncology trials. |
06/09/2017 |
|
Lancet2 Genomics |
Next generation of Lancet, a local-assembly based somatic variant caller for short read sequencing data, with improved runtime and genotyping performance. |
08/23/2023 |
|
Lancet Genomics, Network Biology |
Local-assembly based somatic variant caller for short read sequencing data. Lancet detects somatic SNVs, indels, and more complex mutations by jointly analyzing reads from tumor and matched normal samples using colored de Bruijn graphs. |
07/13/2018 |
|
KSTAR Proteomics |
Prediction of kinase activities from phosphoproteomic data. |
10/13/2021 |
|
KinPred Proteomics |
A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions. |
10/13/2021 |
|
KiNet Pathology Imaging |
KiNet is an open-source software tool for automated Ki67 labeling index assessment in digital pathology images. |
12/10/2021 |
|
JBrowse 2 Visualization |
JBrowse 2 is the new version of the JBrowse genome browser, available as a desktop application, a web application, and embeddable web components. It expands on JBrowse 1 by adding support for showing multiple visualizations, including synteny, circular, breakpoint detail, and tabular views. It also has integrations with Jupyter notebooks and R, and a growing library of plugins. |
07/26/2023 |
|
ivyGlimpse Analysis Platform |
Bioconductor-based interface to Ivy-GAP (glioblastoma.alleninstitute.org) data resources. |
07/14/2017 |
|
International Skin Imaging Collaboration Archive Medical Informatics, Pathology Imaging |
The ISIC Archive is a web-based platform to support the sharing, management and analysis of dermatology imaging data. We currently host over 70,000 public images. The ITCR funding is to support improved dataset curation for various educational and machine learning purposes as well as integration of reflectance confocal microscopy data. |
08/04/2023 |
|
Integrative Genomics Viewer (IGV) Visualization |
Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. It supports flexible integration of common genomic data types, investigator-generated or publicly available, loaded from local or cloud sources. Available in multiple forms: IGV desktop application; igv.js embeddable JavaScript component; IGV-Web in-browser app. |
06/09/2017 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |