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 |
|---|---|---|
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
modelhub.ai Models |
Dissemination Platform for Deep Learning Algorithms. |
06/27/2019 |
|
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 |
|
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 |
|
MethCon5 Epigenetics |
The goal of methcon5 is to identify and rank CpG DNA methylation conservation along the human genome. |
08/28/2020 |