Data Resources

Data Resources - General

• Cancer Research Data Commons 
  • The Cancer Research Data Commons (CRDC) is a centralized location where stakeholders can submit and access multiple curated data repositories

Data Resources - Pre-Clinical

• FlowRepository 
  • FlowRepository is a repository of downloadable, annotated, and peer-reviewed flow cytometry data sets
• immuneACCESS  
  • immuneACCESS is a large repository of T-cell and B-cell receptor sequencing data 
• IOTN Data Sharing Catalog  
  • The IOTN Data Sharing Catalog includes datasets from IOTN awardee publications
•  iReceptor 
  • iReceptor is a repository of antibody/B-cell and T-cell receptor repertoires 
• McPAS-TCR 
  • McPAS-TCR is a curated database of of pathology associated T-cell receptor sequences
•  NCTN/NCORP Data Archive 
  • The NCTN/NCORP Data Archive is a database that includes datasets originating from clinical trials within the National Clinical Trials Network (NCTN) and the NCI Community Oncology Research Program (NCORP)
• VDJdb
  • VDJdb is a curated repository T-cell receptor sequences with known antigen specificities

Data Resources - Data Repositories

• dbGap
  • The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans.
• European Genome-Phenome Archive
  • The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems.
• GEO
  • GEO is a public functional genomics data repository supporting MIAME-compliant data submissions.
• Proteomics Data Commons (PDC) 
  • Clinical Proteomic Tumor Analysis Consortium (CPTAC). 
• The Cancer Imaging Archive (TCIA) 
  • TCIA de-identifies and hosts a large archive of medical images of cancer accessible for public download.
• The NCI's Genomic Data Commons (GDC) 
  • The NCI's GDC provides the cancer research community with a unified repository and cancer knowledge base that enables data sharing across cancer genomic studies in support of precision medicine. 

Software Tools

Software Tools - Framework Software & Libraries

• BioConductor (Tools)  
  • Bioconductor is a R-based toolset used for analysis and comprehension of high-throughput genomic data 

• NCI “Resources for Researchers” 
  • NCI “Resources for Researchers” is a collection of NCI-supported data analysis tools 

• IOTN Bioconductor Suite  
  • The IOTN Bioconductor suite is a collection of Bioconductor tools that can be used for immunotherapy data set analyses 

• IOTN Software Sharing Catalog 
  • The IOTN Software Sharing Catalog is a collection of software programs and source codes from projects supported by IOTN grants 

• SimpleITK 
  • Open-source interface to the Insight Segmentation and Registration Toolkit. The SimpleITK image analysis library is available in multiple programming languages including C++, Python, R, Java, C#, Lua, Ruby and Tcl. 

• OpenCV 
• OpenCV is a library of programming functions mainly aimed at real-time computer vision. 

Software Tools - Cytometry

• CyTOF workflow 
  • CyTOFworkflow is an R-based pipeline used for differential analyses of High-dimensional mass and flow cytometry (HDCyto) data 

• Cytometry dATa anALYSis Tools 
  • CytometrydATa anALYSis Tools (CATALYST) is a tool that provides a pre-processing pipeline and visualization assistance for mass cytometry (CyTOF) data 

• DiffCyt 
  • DiffCytis a bioconductor tool that assists with statistical methods for differential discovery analyses in high-dimensional cytometry data 

• flowCore 
  • FlowCoreis a Bioconductor tool that assists with flow cytometry data analyses 

Software Tools - Single Cell Sequencing

• Kallisto
  • Kallisto is a program used for measuring transcript and/or target sequence abundance in high-throughput sequencing datasets

• Seurat
  • Seurat is an R-based toolkit used for single-cell genomic analyses. Guided analyses forSeruat can be found here 

• Scanpy
  • Scanpy(Single-Cell Analysis in Python) is a Python-based toolkit used for single-cell gene expression analyses 

• Azimuth
  • Reference based cell type annotation forscRNA data 

• Scvi-tools
  • Probabilistic models for single-cell omics data based on auto-encoder neural network models. Dimensionality reduction, dataset integration, differential expression, automated annotation.

Software Tools - Spatial omics & Microscopy Imaging

• cellpose
  • Generalized, machine learning based algorithm for cellsegmentation 

• DeepCelland Mesmer 
  • Deep learning methods for whole cell segmentation

• CytoKit
  • Collection of tools for quantifying and analyzing properties of individual cells in large fluorescent microscopy datasets 

Software Tools - TCR

• FEST 
  • Functional Expansion of Specific T-cells (FEST) is an online program used for analysis of TCR sequencing of short-term, peptide-stimulated cultures in order to identify antigen-specific clonotypic amplifications  

• GLIPH 

• • Grouping of Lymphocyte Interactions by Paratope Hotspots (GLIPH) is an online program used for clustering T-cell receptors based on their predicted MHC-restricted peptide binding properties

• Immunarch 
  • Immunarch is an R based package used for analysis of single-cell and bulk T-cell/antibody repertoires 

• iReceptor 
  • iReceptor is an online platform used for analyzing T-cell receptor and B-cell/antibody repertoire data across federated repositories  

• MiXCR 
  • MiXCR is an online tool used for analysis of raw "Immunome" sequencing data  

• SeeTCR 
  • SeeTCR is an online tool for processing T-cell repertoire data into quantitative graphics  

• VDJServer 
  • VDJServer is an immune repertoire analysis and archiving suite  

• VDJtools 
  • VDJtools is an online tool for analysis of immune repertoire sequencing (RepSeq) data  

• VDJviz 
  • VDJviz is an online browser used to navigate and analyze immune repertoire sequencing data 

Educational Resources

• Analysis of Single-Cell RNA-Seq Data
  • An online course detailing methodology and use for single-cell RNAseq analyses (scRNAseq)

• CITE-Seq
  • CITE-Seq is a method that uses DNA-barcoded antibodies to allow for quantifiable detection of proteins. This website provides introductory education into these techniques.

• Data Carpentry
  • Data Carpentry is an organization that focuses on data science and computational education for researchers

• DataCamp
  • DataCamp is an online data science educational organization, providing both basic and advanced offerings

• SITC-NCI Computational Immuno-Oncology Webinar Series 
  • Free one-hour webinars that focus on computational challenges of analyzing and integrating diverse assay data across the spectrum of immuno-oncology
    
    
• NCI Computational Immuno-oncology (IO) Workshop
  • A workshop to discuss current state of the art technologies, outstanding scientific gaps, and opportunities in computational immuno-oncology (IO)