Informatics Tools

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The ITCR Program funds tools that support the analysis of –omics, imaging, and clinical data, as well as network biology and data standards. 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 below.

Title Description Category Links
GARDE GARDE (Genetic Cancer Risk Detector) is a population clinical decision support (CDS) platform based on Fast Healthcare Interoperability Resources (FHIR) and CDS Hooks standards. GARDE (i) screens and identifies patients who meet National Comprehensive Cancer Network (NCCN) criteria for evaluation of familial cancer risk based on their family history in the EHR; and (ii) promotes genetic testing with eligible patients through a rule-based conversational agent (chatbot) that minimizes genetic counseling workload by automating patient outreach and education. GARDE has been integrated with two market-leading EHR systems (Epic® and Cerner®). GARDE is open source software that can be deployed both through containerization and cloud-based services. GARDE has been deployed in clinical settings at two academic medical centers and their respective cancer centers (University of Utah Health/Huntsman Cancer Institute and New York University Langone Health) in support of the BRIDGE trial, funded by NCI’s Cancer Moonshot program. Clinical, Data Standards
Cancer Models Finder Cancer Models Finder (CancerModels.Org; formerly PDX Finder) is an open global research platform for patient-derived cancer models (PDCMs). It is the largest open catalog of harmonized PDCMs and associated data from academic and commercial providers. -omics
Clinical Interpretation of Variants in Cancer (CIViC) Knowledgebase 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. -omics, Clinical
KiNet KiNet is an open-source software tool for automated Ki67 labeling index assessment in digital pathology images. Imaging
PRECISION.seq PRECISION.seq (PaiREd miCrorna analysIs of differential expresSION for sequencing) enables an objective and systemic evaluation of depth normalization methods in microRNA sequencing based on differential expression status, using realistically distributed and robustly benchmarked data. The package provides a pair of microRNA sequencing data sets for the same set of tumor samples, additional simulated pairs of data sets under various patterns of differential expression, and a collection of numerical and graphical tools for normalization assessment. Users can easily assess their own normalization method and compare its performance to nine popular methods already implemented in the package. -omics
DANA DANA (DAta-driven Normalization Assessment) is an approach for assessing the performance of normalization in a given microRNA-Seq data set, using biology-motivated and data-driven metrics. It takes advantage of well-known biological features of microRNAs for their expression pattern and polycistronic clustering to assess (1) how effectively normalization removes handling effects and (2) how normalization biases true biological signals. In addition to eight commonly used methods that are included in the package, DANA can accommodate any other normalization method as long as the normalized counts are non-negative. -omics
TumorDecon TumorDecon is an open source Python package that includes several deconvolution methods for estimating the relative abundance of cell types in a given tumor from its gene expression profile.  -omics
Ontology for MIcroRNA Target (OMIT) OMIT is a domain ontology specifically designed for the miRNA field. Data Standards
OmniSearch OmniSearch is a semantic search software based upon the OMIT ontology. While OmniSearch is by its nature extensible, its initial focus is in human cancer research. Data Standards
FaNDOM 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. -omics
ecSeg 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. Imaging
AmpliconReconstructor (AR) Reconstructs complex variation and disambiguates Amplicon Architect based reconstructions using BioNano optical mapping data and an NGS-derived breakpoint graph. -omics
AmpliconArchitect (AA) AmpliconArchitect (AA) is a tool which can reconstruct the structure of focally amplified regions in a cancer sample using whole genome sequence short paired-end data. A full description of the methods and detailed characterization of copy number amplifications and ecDNA in cancer can be found in the following manuscript. -omics
Federated Tumor Segmentation (FeTS) The FeTS tool describes an open-source toolkit with a user-friendly graphical user interface (GUI), that aims to i) bring pre-trained segmentation models of numerous deep learning algorithms 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. Imaging
OpenInfobutton 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. Clinical, Data Standards
LesionTracker / OHIF Web Image Viewer 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. Imaging
Globus Globus software services provide secure cancer research data transfer, synchronization, and sharing in distributed environments at large scale. These services can be integrated into applications and research data gateways, leveraging Globus identity management, single sign-on, search, and authorization capabilities. Globus Genomics integrates Globus with the Galaxy genomics workflow engine and Amazon Web Services to enable cancer genomics analysis that can elastically scale compute resources with demand. Imaging, -omics, Clinical, Data Standards, Network Biology
Apache Clinical Text and Knowledge Extration System (cTAKES) and Cancer Deep Phenotype (DeepPhe) The DeepPhe software tools use a combination of natural language processing, machine learning, visual analytics, a rich ontology and ontology-based summarization to extract longitudinal histories from cancer clinical notes. DeepPhe can provide summary phenotype and patient information as well as facilitate retrospective cancer cohort research. Built on the widely-used cTAKES NLP platform, DeepPhe can extract tumor characteristics, treatments, biomarkers and comorbidity information, as well as classify clinical notes in to treatment episodes. DeepPhe can produce results many output formats, as well as store information in a graph database supported by a REST API. Clinical
Galaxy Galaxy is an open-source, Web-based computational workbench for accessible, reproducible, and transparent analyses of high-throughput biomedical data that is used by thousands of scientists across the world. There are more than 8400 analysis tools and 100 visualizations integrated into Galaxy for genomics, image analysis, microbiome, medical informatics, machine learning, drug discovery, and more. Many of Galaxy’s tools are used in cancer informatics research, and new Galaxy tools are being developed by other ITCR projects. Galaxy is being extended to provide cancer researchers with user-friendly tools and visualizations for analyzing cancer datasets distributed across multiple clouds and internal institutional resources. -omics
KSTAR Prediction of kinase activities from phosphoproteomic data. Network Biology
KinPred A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions. -omics, Data Standards, Network Biology
Quantitative Imaging In Pathology (QUIP) QuIP is an integrated software platform designed to support analysis, management, and exploration of whole slide tissue images for cancer research. The QuIP software platform consists of a set of docker containers, which provide analysis execution and data management backend services, and web applications to load and visualize whole slide tissue images (stored in supported file formats)  and explore analysis results. Imaging
CNVnator/CNVpytor A tool for detection of somatic, subclonal, mosaic, and germline CNVs from sequencing -omics
Texomer Texomer deconvolutes allele-specific copy number and mRNA expression levels from paired exome and transcriptome sequencing data of tumor tissue samples and outputs variants associated with tumor specific transcriptional regulation.  -omics
Cancer-Related Analysis of Variants Toolkit (CRAVAT) CRAVAT is a biologist-friendly platform for analysis of coding and non-coding cancer variants and has been extended to create the new Open-Custom Ranked Analysis of VAriants Toolkit, a configurable platform with community-developed annotation, visualization, and analysis tools. OpenCRAVAT provides an app store with 150+ tools, an interactive, richly detailed graphical interface, and is available for local or cloud-based installation. Webserver and Docker versions are also available for CRAVAT and OpenCRAVAT. -omics
RadxTools 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. Imaging
The Cancer Dependency Map Portal The DepMap Portal empowers researchers to make discoveries related to cancer vulnerabilities by providing open access to key datasets, analytical tools, and visualizations. -omics
WebMeV Web MeV (Multiple-experiment Viewer) is a web/cloud-based tool for genomic data analysis. Web MeV is being built to meet the challenge of exploring large public genomic data set with intuitive graphical interface providing access to state-of-the-art analytical tools. -omics
UCSC Xena UCSC Xena securely analyzes and visualizes your private functional genomics data set in the context of public and shared genomic/phenotypic data sets such as TCGA, GDC, ICGC, TARGET, and the UCSC RNA-seq recompute compendium (TCGA + TARGET + GTEx). -omics
Gosling 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. -omics
HemOnc Ontology OMOP-formatted ontology of chemotherapy regimens, their component drugs, and supporting publications, with >87,000 concepts and nearly 240,000 relationships. A portion is available as the HemOnc vocabulary through the vocabulary management tool. The full ontology is freely available to academic and non-commercial users through the CC-BY-NC-SA 4.0 license; a drug-focused subset is available to any user through the CC-BY 4.0 license. Clinical
GenePattern GenePattern is a genomic analysis platform that provides access to hundreds of tools for the analysis and visualization of multiple data types. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. A new GenePattern Notebook environment allows users to combine GenePattern analyses with text, graphics, and code to create complete reproducible research narratives. -omics
cBioPortal for Cancer Genomics The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.  -omics
Trinity Trinity Cancer Transcriptome Analysis Toolkit (CTAT) including de novo transcriptome assembly with downstream support for expression analysis and focused analyses on cancer transcriptomes, incorporating mutation and fusion transcript discovery, and single cell analysis. -omics
Cistrome Explorer Cistrome Explorer is an interactive and scalable visual analytics tool for analyzing chromatin accessibility, histone modification, and transcription factor binding data with associated metadata. Cistrome Explorer can be used for visualizing more than 200 experimental samples at once on a genome-wide scale to facilitate the comparison of patterns between large numbers of cell types and conditions. Moreover, Cistrome Data Browser Toolkit is intergrated into Cistrome Explorer to enable searching for transcription factors that are most likely to bind in a genomic region of interest or near a gene of interest. -omics
Next Generation Clustered Heat Maps 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. -omics
QIIME 2 QIIME 2 is a microbiome bioinformatics platform that is widely used for investigation of the human microbiome, including studies investigating how our microbiota may impact carcinogenesis, how microbiota may impact the efficacy of cancer treatment, how cancer treatment may impact the microbiota, and associations between the microbiome and cancer prognosis. QIIME 2 was designed to ensure reproducible bioinformatics through its unqiue retrospective data provenance tracking system, and to facilitate accessibility to users with varying degrees of computational sophistication. QIIME 2 takes users from raw data through publication quality visualizations and statistics. -omics, Network Biology
Bioconductor Bioconductor enables statistical analysis of cancer genomic data. Basic researchers (e.g., bioinformaticians and statisticians) use Bioconductor to translate experimental results into actionable biological understanding. An example is to relate gene expression in ‘tumor’ and ‘normal’ tissues to mutations and biochemical pathways that influence cancer. Bioconductor is highly impactful, with thousands of users in academic, government, and industry labs contributing to scientific publications and large-scale collaborative efforts to understand and treat cancer. -omics
OncoMX OncoMX is a cancer biomarker database with mutation and expression metadata related to the study of cancer alongside relevant experimental and functional annotations. -omics
MethCon5 The goal of methcon5 is to identify and rank CpG DNA methylation conservation along the human genome. -omics
Integrative Genomics Viewer (IGV) The 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 all the common types of genomic data and metadata, investigator-generated or publicly available, loaded from local or cloud sources. IGV is available in multiple forms: the original IGV desktop application, the igv.js JavaScript component for embedding in web pages, and the IGV-Web app that runs in a web browser. -omics
Tools for neoantigen characterization and personalized cancer vaccine design (pVACtools) Neoantigens are tumor specific antigens arising from somatic mutations that, when identified accurately, can be high value targets for cancer immunotherapy. pVACtools is an open source, open access suite of informatics tools that enables identification, prioritization, and clinical application of neoantigens. pVACtools is currently being extended to support all major sources of neoantigens, integrate analysis of MHC Class I and II binding, discover new factors that influence immunogenicity, and use this knowledge to better prioritize neoantigen candidates. -omics, Clinical
BioMuta Cancer associated gene mutation -omics
The Cancer Imaging Archive (TCIA) TCIA is NCI’s repository for publicly shared cancer imaging data. TCIA collections include radiology and pathology images, clinical and clinical trial data, image derived annotations and quantitative features and a growing collection of related ‘omics data both from clinical and pre-clinical studies. Imaging
AMARETTO AMARETTO for multi-omics data fusion and reformulations for pan-etiology and pan-cancer applications. -omics
dcmqi: DICOM for Quantitative Imaging dcmqi is a free, open source library that implements conversion of the data stored in commonly used research formats into the standard DICOM representation Data Standards, Imaging
Tools for Quantitative Analysis of PET Imaging A collection of extensions for 3D Slicer to enable quantitative analysis of PET imaging data: image normalization, segmentation, and extraction of quantitative indices. Imaging
CLAMP-Cancer 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 Clinical
Tumor Heterogenity Research Interactive Visualization Environment (THRIVE) A platform for quantitative evaluation of intratumoral spatial heterogeneity in multiplexed immunofluorescence images, via characterization of the spatial interactions between different cellular phenotypes and non-cellular constituents in the tumor microenvironment. A plugin mechanism enables researches to add and share their own heterogeneity algorithms. Imaging
Single Cell Genome Viewer (SCGV) Graphics user interface for single-cell genomics -omics
Cloud-based Image Biomarker Platform (C-BIBOP) C-BIBOP is a cloud based platform for medical imaging algorithm comparisons. C-BIBOP is used to conduct challenges and benchmarks and uses Docker containers to share algorithm. Imaging
ivyGlimpse Bioconductor-based interface to Ivy-GAP ( data resources Imaging, -omics
The Cancer Proteome Atlas The Cancer Proteome Atals is a comprehensive bioinformatic resource for assessing, visualzing and analyzing the functional proteomics data of patient tumor and cell line samples. -omics
DINC 2.0 DINC 2.0 is a parallelized meta-docking method for the incremental docking of large ligands (currently using AutoDock Vina) -omics
PhenStat PhenStat is a freely available R package that provides a variety of statistical methods for the identification of phenotypic associations from model organisms developed for the International Mouse Phenotyping Consortium (IMPC at ). The methods have been developed for high throughput phenotyping pipelines implemented across various experimental designs with an emphasis on managing temporal variation and is being adapted for analysis with PDX mouse strains. -omics is a open source platform for informatics developments for radiographic phenotyping using automated algorithms, such as engineered features or using deep learning technologies. With this platform, we aim to establish a reference standard for radiomic analyses, provide a tested and maintained resource, and to grow the community of radiomic developers addressing critical needs in cancer research. Imaging
SampleMap Projects samples into a GoogleMap explorer to allow overlaying omics attributes to spot patterns quickly. A TumorMap version was built for TCGA analysis. -omics
Pathology Imaging Informatics Platform (PIIP) 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. Imaging
FHIR ShEx ShEx is a QA tool based on the Shape Expressions Language that is an emerging W3C standard to validate RDF graphs. Data Standards
SlicerDMRI Diffusion magnetic resonance imaging for neurosurgical planning in 3D Slicer open-source software. Imaging
The Laboratory for Individualized Breast Radiodensity Assessment (LIBRA) LIBRA is a fully-automatic breast density estimation software solution based on a published algorithm that works on either raw (i.e., “FOR PROCESSING”) or vendor post-processed (i.e., “FOR PRESENTATION”) digital mammography images. LIBRA has been applied to over 30,000 screening exams and is being increasingly utilized in larger studies. Imaging
XNAT XNAT is an open source imaging informatics platform designed to support institutional image repositories, image-based clinical trials, and translational imaging research. Imaging
Methylation Integration (Mint) 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. -omics
NDEx - The Network Data Exchange NDEx is an online commons where scientists can upload, share, and publicly distribute biological networks and pathway models. The NDEx Project maintains a web-accessible public server, a documentation website, provides seamless connectivity to Cytoscape as well as programmatic access using a variety of languages including Python and Java. NDEx  users can easily create accounts or sign in using their Google credentials thanks to  the supported open authentication (OAUTH2) method  and mint DOIs for their networks to use in publications or include in other resources for long term access.  Network Biology
owl-qa owl-qa is an OWL-based QA tool for cancer study CDEs. The tool uses the combination of the NCI Thesaurus and additional disjointness axioms to detect potential errors and duplications in the data element definitions. The tool comprises three modules: Data Integration and Services Module; Compositional Expression Transformation Module; and OWL-based Quality Assurance Module. Data Standards
P-Mart Web-based software platform to enable analysis and exploration of publicly available cancer proteomic datasets, such as those generated by the CPTAC program. -omics
Personalized Cancer Therapy Curated website cataloguing clinically actionable information for personalized cancer therapy including clinically significant genetic variants and drug-gene association. Clinical, -omics
Cores Of Recurrent Events (CORE) 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. -omics
D2Refine D2Refine is an integrated platform that enables cancer study data/metadata harmonization and quality assurance. The platform is based on the Open Refine and enhanced with a suite of plugins. Data Standards
DICOM ToolKit (DCMTK) DCMTK is an open source DICOM toolkit. Imaging, Data Standards
Enhancer Linking by Methylation/Expression Relationships (ELMER) 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. -omics
Galaxy-P multi-omics A unified platform for integrative genomic-proteomic-metabolomic data analysis and informatics in cancer research. -omics
Cancer Slide Digital Archive (CDSA) The CDSA is a web-based platform to support the sharing, managment and analysis of digital pathology data. The Emory Instance currently hosts over 23,000 images from The Cancer Genome Atlas, and the software is being developed within the ITCR grant to be deployable as a digital pathology platform for other labs and Cancer Institutes. Imaging
Cistrome 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. -omics
3D Slicer 3D Slicer is the free open source software for medical image visualization and analysis. Imaging
Cancer Imaging Phenomics Toolkit (CaPTk) CaPTk is a software toolkit to facilitate translation of quantitative image analysis methods that help us obtain rich imaging phenotypic signatures of oncologic images and relate them to precision diagnostics and prediction of clinical outcomes, as well as to underlying molecular characteristics of cancer. The stand-alone graphical user interface of CaPTk brings analysis methods from the realm of medical imaging research to the clinic, and will be extended to use web-based services for computationally-demanding pipelines. CaPTk replicates basic interactive functionalities of radiological workstations and is distributed under a BSD-style license. Youtube: Imaging
Gene Set Enrichment Analysis (GSEA) and Molecular Signatures Database (MSigDB) GSEA is an open source software tool for the analysis of global transcription profiling data, available as a standalone desktop application and as GenePattern modules. The underlying method determines whether a given gene set, corresponding to a biological process, pathway, phenotype or cellular perturbation, is significantly coordinately up- or down-regulated and thus shed light on underlying mechanism. It can be used to compare phenotypes or used on individual samples. The software provides useful visualizations and reports for interpretation of results. The MSigDB is a companion resource of annotated gene sets for use with GSEA. -omics
HistoQC 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.  Imaging, Data Standards Dissemination Platform for Deep Learning Algorithms -omics
Integrated Methods for Predicting Enhancer Targets (IM-PET) 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. -omics
Gaussian Mixture Model and Proportion Test (GMAP) 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. -omics
The JBrowse Genome Browser JBrowse is an open access, fast, and scalable genome browser built using JavaScript and HTML5. The mission of JBrowse is to make genome annotations and sequence analysis tools more accessible to the broader community of biologists. Designed to run on your desktop or be embedded in your website, JBrowse supports a wide range of data types in a variety of common genomic data formats and software plugins to configure the appearance and behavior of the graphical interface. -omics
TOPAS Monte Carlo simulation of ionizing radiation transport for medical applications with focus on therapy and imaging with x-rays, electrons, protons and all other forms of ionizing radiation. Imaging, Clinical
Electronic Medical Record Search Engine (EMERSE) EMERSE is an intuitive, user-friendly, and powerful search engine for free text documents from electronic health record (EHR) systems.  It can be used for a wide variety of tasks including cohort identification, eligibility determination, looking for adverse events, and general data abstraction needs to support clinical and translational research. It has powerful features like the ability to limit searches to user-defined patient lists, and a powerful query expansion/synonym suggestion feature. Clinical
Integrative Genomics Robust iDentification of cancer subgroups (InGRiD) 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. -omics
Lancet 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. -omics
Quantitative Image Informatics for Cancer Research (QIICR) Tools Catalog A collection of tools to promote the adoption of quantitative imaging tools and DICOM standard in medical imaging research. Imaging