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 |
|---|---|---|
|
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 |
|
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 |
|
ivyGlimpse Analysis Platform |
Bioconductor-based interface to Ivy-GAP (glioblastoma.alleninstitute.org) data resources. |
07/14/2017 |
|
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 |
|
KiNet Pathology Imaging |
KiNet is an open-source software tool for automated Ki67 labeling index assessment in digital pathology images. |
12/10/2021 |
|
KinPred Proteomics |
A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions. |
10/13/2021 |
|
KSTAR Proteomics |
Prediction of kinase activities from phosphoproteomic data. |
10/13/2021 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
MethCon5 Epigenetics |
The goal of methcon5 is to identify and rank CpG DNA methylation conservation along the human genome. |
08/28/2020 |
|
Methylation Integration (Mint) Epigenetics |
A comprehensive software pipeline and set of Galaxy tools/workflows for integrative analysis of genome-wide DNA methylation and hydroxymethylation data. Data types can be either bisulfite sequencing and/or pull-down methods. |
06/09/2017 |
|
MIRA: Multimodal models for Integrated Regulatory Analysis Epigenetics, Transcriptomics |
MIRA is a Python software package for analyzing single cell RNA-seq, ATAC-seq and multimodal data. MIRA includes effective batch correction methods for both modalities and infers gene regulatory mechanisms and regulatory transcription factors through integrative analyses of joint RNA and chromatin accessibility modalities. |
07/26/2023 |
|
modelhub.ai Models |
Dissemination Platform for Deep Learning Algorithms. |
06/27/2019 |
|
NDEx - The Network Data Exchange Network Biology |
NDEx, The Network Data Exchange, is an online data commons where scientists can upload, share, and publicly distribute biological networks and pathway models. It also provides the NDEx IQuery gene set analysis web app based on NDEx networks. Developers can integrate their programs and web applications with NDEx and IQuery. |
06/09/2017 |
|
Network Analysis of Immune Repertoire (NAIR) Immuno-oncology |
NAIR, Network Analysis of Immune Repertoire, is an R package using network analysis and machine learning to explore immune receptor (TCR/BCR) sequences. Users can search and visualize disease-associated/shared sequence clusters and perform downstream analysis. It supports amino acid and nucleotide sequences, multiple distance metrics, and bulk and single-cell data. |
09/19/2023 |
|
Next Generation Clustered Heat Maps Visualization |
Next-Generation (Clustered) Heat Maps are interactive heat maps that enable the user to zoom and pan across the heatmap, alter its color scheme, generate production quality PDFs, and link out from rows, columns, and individual heatmap entries to related statistics, databases and other information. |
06/09/2017 |
|
OncoMX Analysis Platform, Visualization |
OncoMX is a cancer biomarker database with mutation and expression metadata related to the study of cancer alongside relevant experimental and functional annotations. |
08/16/2019 |