Informatics Tools

Tool Namesort descending Categories Description Relevant Links
3D Slicer Imaging 3D Slicer is the free open source software for medical image visualization and analysis.
Allele-Specific Alternative mRNA Processing (ASARP) OMICS 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.
Apache Clinical Text and Knowledge Extraction System (cTAKES) Clinical 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.
Bioconductor OMICS 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.
C-BIBOP Imaging 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.
Cancer and Phenomics Toolkit (CaPTk) Imaging CaPTk is a tool that facilitates translation of highly sophisticated methods that help us gain a comprehensive understanding of the underlying mechanisms of cancer from medical imaging research to the clinic. It replicates basic interactive functionalities of radiological workstations and is distributed under a BSD-style license.
Cancer Slide Digital Archive (CDSA) Imaging 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.
Cancer-Related Analysis of VAriants Toolkit (CRAVAT) OMICS 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 avariety of annotations that assist in identification of important variants. In addition to the webservice, CRAVAT is also available for local or cloud-based installation as a docker container.”
Cistrome OMICS 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.
Clinical Interpretation of Variants in Cancer (CIViC) Knowledgebase Clinical,
OMICS 		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.
Cores Of Recurrent Events (CORE) OMICS 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.
D2Refine Data Standards 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.
DICOM ToolKit (DCMTK) Imaging DCMTK is an open source DICOM toolkit.
Enhancer Linking by Methylation/Expression Relationships (ELMER) OMICS 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.
Feature DB Imaging The backend database to manage segmentation results, computed image features and annotations. FeatureDB drives the database for the QUIP web-platform.
Galaxy-P multi-omics OMICS A unified platform for integrative genomic-proteomic-metabolomic data analysis and informatics in cancer research.
GenePattern OMICS 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.
Genome-Independent Identification of RNA Editing by Mutual Information (GIREMI) OMICS 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.
Integrative Genomics Viewer (IGV) OMICS 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.
LSTM-CRF Clinical 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.
Methylation Integration (Mint) OMICS 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.
Modified UMS, Modified SemRep and SemMedDB-UTH Clinical,
OMICS 		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.
Mutated Positions in Annotated Structures (MuPIT) OMICS MuPIT provides 3D visualization of mutation clusters and functional annotation.
NDEx - The Network Data Exchange Network Biology 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.
Next Generation Clustered Heat Maps OMICS 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.
OmniSearch Data Standards 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.
Ontology for MIcroRNA Target (OMIT) Data Standards OMIT is a domain ontology specifically designed for the miRNA field.
Open Health Imaging Foundation (OHIF) viewer 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.
owl-qa Data Standards 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.
P-Mart OMICS Web-based software platform to enable analysis and exploration of publicly available cancer proteomic datasets, such as those generated by the CPTAC program.
Personalized Cancer Therapy Clinical,
OMICS 		Curated website cataloguing clinically actionable information for personalized cancer therapy including clinically significant genetic variants and drug-gene association.
PhenStat OMICS 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.
Quantitative Imaging In Pathology (QUIP) Imaging This site hosts web accessible applications, tools and data designed to support analysis, management, and exploration of whole slide tissue images for cancer research. The following tools are included: caMicroscope: A digital pathology data management and visualization plaform that enables interactive viewing of whole slide tissue images and segmentation results. caMicroscope can be also used independently of QUIP. FeatureExplorer: An interactive tool to allow patient-level feature exploration across multiple dimensions. FeatureScape: A visual analytics platform for exploring imaging features generated by analysis of whole slide tissue images.
RADIOMICS.io Imaging 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.
Region Templates Imaging A suite of libraries and runtime to support image analysis.
SampleMap OMICS Projects samples into a GoogleMap explorer to allow overlaying omics attributes to spot patterns quickly. A TumorMap version was built for TCGA analysis.
Sedeen viewer 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.
ShEx Data Standards ShEx is a QA tool based on the Shape Expressions Language that is an emerging W3C standard to validate RDF graphs.
SlicerDMRI Imaging Diffusion magnetic resonance imaging for neurosurgical planning in 3D Slicer open-source software.
Text Information Extraction System (TIES) Clinical 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.
The Laboratory for Individualized Breast Radiodensity Assessment (LIBRA) Imaging 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.
Trinity OMICS 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.
UCSC Xena OMICS 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, ICGC, TARGET, GTEx, and BD2K-GA4GH (TOIL).
WebMeV OMICS 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.
XNAT Imaging XNAT is an open source imaging informatics platform designed to support institutional image repositories, image-based clinical trials, and translational imaging research.