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.

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  • 3D Slicer
    3D Slicer is the free open source software for medical image visualization and analysis.
    Category:
    Imaging
    imaging
  • Allele-Specific Alternative mRNA processing (ASARP)
    A software pipeline for prediction of allele-specific alternative RNA processing events using single RNA-seq data. The current version focuses on prediction of alternative splicing and alternative polyadenylation modulated by genetic variants.
    Category:
    -omics
    -omics
  • Apache Clinical Text and Knowledge Extration System (cTAKES) and Cancer Deep Phenotype (DeepPhe)
    The tool extracts deep phenotypic information from the clinical narrative at the document-, episode-, and patient-level. The final output is FHIR compliant patient-level phenotypic summary which can be consumed by research warehouses or the DeepPhe native visualization tool.
    Category:
    Clinical
    clinical
  • Bioconductor
    Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. R/Bioconductor will be enhanced to meet the increasing complexity of multiassay cancer genomics experiments.
    Category:
    -omics
    -omics
  • 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: https://www.youtube.com/channel/UC69N7TN5bH2onj4dHcPLxxA
    Category:
    Imaging
    imaging
  • 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.
    Category:
    Imaging
    imaging
  • Cancer-Related Analysis of Variants Toolkit (CRAVAT)
    CRAVAT is an easy to use web-based tool for analysis of cancer variants (missense, nonsense, in-frame indel, frameshift indel, splice site). CRAVAT provides scores and a variety of annotations that assist in identification of important variants. Results are provided in an interactive, highly graphical webpage and include annotated 3D structure visualization.  CRAVAT is also available for local or cloud-based installation as a Docker container.  Finally, our new Open-Custom Ranked Analysis of VArants Toolkit is a configurable python package with community developed analysis modules.
    Category:
    -omics
    -omics
  • 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.
    Category:
    -omics
    -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.
    Category:
    -omics, Clinical
    -omics
    clinical
  • 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.
    Category:
    -omics
    -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.
    Category:
    Data Standards
    data-standards
  • DICOM ToolKit (DCMTK)
    DCMTK is an open source DICOM toolkit.
    Category:
    Imaging, Data Standards
    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.
    Category:
    -omics
    -omics
  • Feature DB
    The backend database to manage segmentation results, computed image features and annotations. FeatureDB drives the database for the QUIP web-platform.
    Category:
    Imaging
    imaging
  • Galaxy-P multi-omics
    A unified platform for integrative genomic-proteomic-metabolomic data analysis and informatics in cancer research.
    Category:
    -omics
    -omics
  • 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.
    Category:
    -omics
    -omics
  • Genome-Independent Identification of RNA Editing by Mutual Information (GIREMI)
    Identification of single-nucleotide variants in RNA-seq data. Current version focuses on detection of RNA editing sites without requiring genome sequence data. New version is under development to separately identify RNA editing sites and genetic variants using RNA-seq data alone.
    Category:
    -omics
    -omics
  • Integrative Genomics Viewer (IGV)
    The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
    Category:
    -omics
    -omics
  • LSTM-CRF
    LSTM-CRF uses Natural Language Processing methods for detecting Adverse Drug Events, Drugname, Indication and other medically relevant information from Electronic Health Records. It implements Recurrent Neural Networks using several CRF based inference methods.
    Category:
    Clinical
    clinical
  • 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.
    Category:
    -omics
    -omics
  • Modified UMS, Modified SemRep and SemMedDB-UTH
    Modified UMLS, modified SemRep and SemMedDB-UTH – these are resources (UMLS, SemMedDB-UT) and tools (SemRep) created and maintained by National Library of Medicine that we have modified for personalized cancer therapy and returned to the NLM.
    Category:
    Clinical, -omics
    clinical
    -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. 
    Category:
    Network Biology
    network-biology
  • 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.
    Category:
    -omics
    -omics
  • 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.
    Category:
    Data Standards
    data-standards
  • Ontology for MIcroRNA Target (OMIT)
    OMIT is a domain ontology specifically designed for the miRNA field.
    Category:
    Data Standards
    data-standards
  • LesionTracker 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.
    Category:
    Imaging
    imaging
  • 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.
    Category:
    Data Standards
    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.
    Category:
    -omics
    -omics
  • Personalized Cancer Therapy
    Curated website cataloguing clinically actionable information for personalized cancer therapy including clinically significant genetic variants and drug-gene association.
    Category:
    Clinical, -omics
    clinical
    -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 www.mousephenotype.org ). 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.
    Category:
    -omics
    -omics
  • 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.
    Category:
    Imaging
    imaging
  • RADIOMICS.io
    RADIOMICS.io 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.
    Category:
    Imaging
    imaging
  • Region Templates
    A suite of libraries and runtime to support image analysis.
    Category:
    Imaging
    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.
    Category:
    -omics
    -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.
    Category:
    Imaging
    imaging
  • FHIR ShEx
    ShEx is a QA tool based on the Shape Expressions Language that is an emerging W3C standard to validate RDF graphs.
    Category:
    Data Standards
    data-standards
  • SlicerDMRI
    Diffusion magnetic resonance imaging for neurosurgical planning in 3D Slicer open-source software.
    Category:
    Imaging
    imaging
  • Text Information Extraction System (TIES)
    TIES is a service based software system for acquiring, deidentifying, and processing clinical text reports using natural language processing, and also for querying, sharing and using this data to foster tissue and image based research, within and between institutions.
    Category:
    Clinical
    clinical
  • 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.
    Category:
    Imaging
    imaging
  • 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.
    Category:
    -omics
    -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)
    Category:
    -omics
    -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.
    Category:
    -omics
    -omics
  • XNAT
    XNAT is an open source imaging informatics platform designed to support institutional image repositories, image-based clinical trials, and translational imaging research.
    Category:
    Imaging
    imaging
  • 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.
    Category:
    Imaging
    imaging
  • ivyGlimpse
    Bioconductor-based interface to Ivy-GAP (glioblastoma.alleninstitute.org) data resources
    Category:
    Imaging, -omics
    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.
    Category:
    -omics
    -omics
  • DINC 2.0
    DINC 2.0 is a parallelized meta-docking method for the incremental docking of large ligands (currently using AutoDock Vina)
    Category:
    -omics
    -omics
  • AMARETTO
    AMARETTO for multi-omics data fusion and reformulations for pan-etiology and pan-cancer applications.
    Category:
    -omics
    -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
    Category:
    Data Standards, Imaging
    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.
    Category:
    Imaging
    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
    Category:
    Clinical
    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.
    Category:
    Imaging
    imaging
  • PETCT-CoSeg
    A PET-CT co-segmentation tool for tumor delineation.
    Category:
    Imaging
    imaging
  • Single Cell Genome Viewer (SCGV)
    Graphics user interface for single-cell genomics
    Category:
    -omics
    -omics
  • BioMuta
    Cancer associated gene mutation
    Category:
    -omics
    -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.
    Category:
    Imaging
    imaging
  • cBioPortal for Cancer Genomics
    The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. 
    Category:
    -omics
    -omics
  • Patient-Derived Xenograft (PDX) Finder
    PDX Finder is a freely available resource that is integrating, archiving and disseminating information about Patient Derived Xenograft models and their associated data.
    Category:
    -omics
    -omics
  • The BioMedical Evidence Graph (BMEG)
    The BMEG is a Cancer Data integration Platform that utilizes methods collected from DREAM challenges and applied to large datasets, such as the TCGA, and makes them avalible for analysis using a high performance graph database
    Category:
    -omics
    -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.
    Category:
    Imaging
    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.
    Category:
    Imaging, -omics, Clinical, Data Standards, Network Biology
    imaging
    -omics
    clinical
    data-standards
    network-biology
  • 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.
    Category:
    -omics
    -omics
  • HemOnc Vocabulary
    OMOP-formatted ontology of chemotherapy regimens, their component drugs, and supporting publications, with >76,000 concepts and >180,000 relationships. A portion is available as the HemOnc vocabulary through the athena.ohdsi.org vocabulary management tool. The full ontology is freely available upon request to academic and non-commercial users through the CC-NC-SA 4.0 license.
    Category:
    Clinical
    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.
    Category:
    Clinical
    clinical
  • OpenCDS
    OpenCDS is an open-source framework for enabling standards-based clinical decision support (CDS).  It supports HL7 standards including FHIR and CDS Hooks.  It is being used within the ITCR grant to support personalized risk assessment for early-onset breast and colorectal cancer.
    Category:
    Clinical, Data Standards
    clinical
    data-standards
  • 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.
    Category:
    Clinical, Data Standards
    clinical
    data-standards
  • 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.
    Category:
    -omics
    -omics
  • Gene-gene Association Inference based on biomedical Literature (GAIL)
    GAIL (Gene-gene Association Inference based on biomedical Literature) is a web interface and database that allow investigation, visualization, and mining of human gene-gene networks based on the PubMed articles.
    Category:
    -omics
    -omics
  • Patient-Specific Drug-Gene Networks for Recommending Targeted Cancer Therapies (CDGnet)
    CDGnet is a tool for prioritizing targeted therapies based on an individual's tumor profile. Tumor molecular profiling refers to the use of a panel of genes and proteins that are assessed for potential abnormalities, including genetic changes and over/under expression of genes or proteins, in order to decide on targeted treatment plans. CDGnet incorporates information from biological networks relevant to the cancer type and to the specific alterations, FDA-approved targeted cancer therapies and indications, additional gene-drug information, and data on whether given genes are oncogenes.
    Category:
    -omics, Clinical, Network Biology
    -omics
    clinical
    network-biology
  • CNVnator
    A tool for detection of somatic, subclonal, mosaic, and germline CNVs from sequencing
    Category:
    -omics
    -omics
  • 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.
    Category:
    -omics
    -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.
    Category:
    Imaging, Clinical
    imaging
    clinical
  • 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.
    Category:
    -omics
    -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.
    Category:
    -omics
    -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.
    Category:
    -omics
    -omics
  • modelhub.ai
    Dissemination Platform for Deep Learning Algorithms
    Category:
    -omics
    -omics
  • OncoMX
    OncoMX is a cancer mutation and expression knowledgebase developed to enable exploration of cancer biomarkers alongside relevant experimental evidence and functional annotations.
    Category:
    -omics
    -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. 
    Category:
    Imaging, Data Standards
    imaging
    data-standards
  • Galaxy
    Galaxy is an open-source, Web-based computational workbench for accessible, reproducible, and transparent analyses of high-throughput biomedical data. There are more than 7300 analysis tools and 100 visualizations integrated into Galaxy for genomics, image analysis, microbiome, medical informatics, machine learning, drug discovery, and more. Galaxy will be extended to provide cancer researchers with user-friendly tools and visualizations for effectively analyzing cancer datasets distributed across multiple clouds and internal institutional resources.
    Category:
    -omics
    -omics