NCI Scientific Applications (Analysis Tools and Portals)

3DVizSNP enables rapid screening of mutations extracted from a variant caller format (VCF) file using the iCn3D protein structure and sequence viewing platform. All you need is a VCF file and you’re ready to go!

The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, or proteogenomics. This cProSite tool is to use data from CPTAC to build a web based interactive platform for data analysis.

A Web Tool to explore the clinically-reportable assay that uses genome-wide DNA methylation profiling as a diagnostic tool for tumors of the central nervous system.

MAAPster is a comprehensive web tool designed by the CCR Collaborative Bioinformatics Resource (CCBR) that performs transcriptome analysis of human or mouse Affymetrix gene expression data. Samples may be uploaded locally or accessed from published data by entering a GEO Series identification number. MAAPster can analyze data from a single experiment that includes multiple samples, and the user may investigate multiple contrasts between groups of samples. Raw CEL files are analyzed using several Bioconductor packages in ‘R’, including limma and oligo. Output includes quality control plots, differential gene expression analysis, gene expression heatmaps, pathway analysis and single sample GSEA analysis.

The scAtlasLC (single-cell Atlas in Liver Cancer) tool is a publicly available data portal of single-cell transcriptomic profiles of tumor cell communities in hepatocellular carcinoma and intrahepatic cholangiocarcinoma.

Explore epidemiological outcomes for target populations with the CC3S Cervical Cancer Screening Scenario Simulator.

A web portal for ICRP that enables senior representatives of cancer research funding organizations to connect, network, and collaborate to enhance global cancer research.

COMETS Analytics supports and streamlines consortium-based analyses of metabolomics and other -omics data. COMET Analytics was designed to simplify meta-analysis at the consortia level. Users prepare data input, and then the software verifies data integrity, performs data analyses securely, and aggregates results in a standardized format.

CEDCD contains descriptive information about cohort studies that follow groups of persons over time for cancer incidence, mortality, and other health outcomes. CEDCD is a searchable database that contains general study information (e.g., eligibility criteria and size), the type of data collected at baseline, cancer sites, number of participants diagnosed with cancer, and biospecimen information. All data included in this database are aggregated for each cohort; there are no individual level data. The goal of the CEDCD is to facilitate collaboration and highlight the opportunities for research within existing cohort studies.

JPSurv is a tool for estimating and presenting survival trend. It can be used to predict survival in any given year and any time interval. Two implemented statistical methods are joinpoint survival model and trend measures. Five supported types of trend measures are Annual percentage changes of hazard, Annual percentage changes of cumulative relative survival, Annual changes of cumulative relative survival, Average annual absolute percent changes, and Average annual relative percent changes.

This tool has been developed to estimate the risk of progressing to distant recurrence using disease-specific survival typically provided by cancer registries. The disease-specific survival is assessed via cause-specific survival using SEER*Stat software.The cause-specific survival is assumed to follow a mixture-cure model and the risk of recurrence is inferred from the survival among the non-cured fraction. The cure fraction and parametric survival distribution among those not cured are estimated using CanSurv software. The current version can handle Weibull and log-logistic distributions for the non-cured survival.

Activities Completed over Time in 24 hours (ACT24) is a web-based previous-day recall instrument that was designed to estimate daily summary values for physical activity and sedentary behavior, including energy expenditure, time spent sitting and in different types and intensities of physical activity.

Age Period Cohort (APC) analysis identifies patterns in cancer incidence or mortality rates from population-based Count (numerator) and Population (denominator) data. Often the data come from a Cancer Registry (e.g., SEER) in the form of a table showing the numbers of cancer cases or cancer deaths (counts) and corresponding person-years at risk (population) for particular age groups and calendar time periods. This toolset provides a comprehensive solution to age-period-cohort analysis for cancer endpoints in defined populations and time periods.

AuthorArranger is a free web tool designed to help authors of research manuscripts automatically generate correctly formatted title pages for manuscript journal submission in a fraction of the time it takes to create the pages manually. Whether your manuscript has 20 authors or 200, AuthorArranger can save you time and resources by helping you conquer journal title pages in seconds.

The Breast Cancer Risk Assessment Tool (BCRAT) is an interactive tool designed by scientists at the National Cancer Institute (NCI) and the National Surgical Adjuvant Breast and Bowel Project (NSABP) to estimate a woman's risk of developing invasive breast cancer.

This toolset estimates risk stratification from early biomarker data and includes math and strategies to advance biomarkers or other risk measures identified case-control studies to clinical or public health applications. The toolset will show quantities for which people's intuition is poor, such as need for high specificity for a single marker of a rare disease to improve management by some serious intervention.

The toolset will allow to evaluate the feasibility of biomarkers called promising before they get press office attention; investigators spend efforts on hopeless pursuit; wasteful. unethical clinical testing begins. Thus, using these strategies will allow focusing on the most promising markers early on, making specific improvements if required, or abandoning markers that are most likely to fail.

The Colorectal Risk Assessment Tool (CCRAT) is a tool designed for doctors and health providers to use along with their patients to determine their risk for developing colorectal cancer.

TThe Chernobyl (Chornobyl in Ukrainian) Tissue Bank (CTB) is a repository of samples donated by patients with thyroid tumors who live in the areas affected by the accident at the Chernobyl Nuclear Power Plant. The purpose of the CTB is to collect, document, and store these materials, and to facilitate access to these unique resources by bona fide researchers.

A web-based tool for integrative Quantitative Trait Loci (QTL) visualization and colocalization with GWAS data for individual loci to aid GWAS annotation.

A web-based tool designed to enable the exploration of DNase I tag (chromatin accessibility) signal surrounding GWAS array SNPs and the calculation of significance of overlap with transcription factor binding sites from common TF databases.

FORGEdb is a tool that consolidates diverse data on disease-related genetic variants, presenting it with a functional importance score to guide further research.

GWAS Explorer serves as an interactive resource for genetics researchers as well as other interested individuals to search for, visualize, and download aggregated association results from genome-wide association studies (GWAS) analyses.

A comprehensive resource and web tool for identification of target genes and pathways from genome-wide association studies (GWAS) data.

ICD Genie is a web-based tool that can assist epidemiologists, pathologists, research assistants, and data scientists to more easily access, translate and validate codes and text descriptions from the International Classification of Diseases (10th Edition) and International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3).

A suite of web-based applications designed to easily and efficiently explore linkage disequilibrium in population subgroups. All population genotype data originates from Phase 3 of the 1000 Genomes Project and variant RS numbers are indexed based on dbSNP build 151.

The Melanoma Risk Assessment Tool (MRAT) is an interactive tool designed by scientists at the National Cancer Institute (NCI), the University of Pennsylvania, and the University of California, San Francisco, to estimate a person's absolute risk of developing invasive melanoma. The tool helps clinicians identify individuals at increased risk of melanoma in order to plan appropriate screening interventions with them.

A web-based tool designed to provide state-of-the art methods to explore, visualize and analyze mutational signatures, which will greatly facilitate broad investigation of mutational signatures to elucidate different mutagenesis processes involved in tumorigenesis.

A web-based educational tool with a collection of pictures assembled to help patients and others in the lay public recognize dysplastic nevi and melanomas that started in dysplastic nevi. Dysplastic nevi (DN) are atypical moles that are important risk markers for melanoma, and precursor lesions for some melanomas.

The web tool, PIMixture estimates the absolute risk of asymptomatic disease or disease precursors. Because asymptomatic disease/disease precursors are often discovered through screening, collected data may present challenges for absolute and relative risk estimation.

A Standardized Occupation Coding for computer-assisted epidemiologic research (SOCcer) is a web tool to assist epidemiological researchers in incorporating occupational risk into their studies, SOCcer imports free-text job descriptions and suggests the best-fitting SOC-2010 standardized occupation classification code for each job. The application is not intended to replace expert coders but rather prioritizes job descriptions that would most benefit from expert coders.

A web-based tool to estimate the power of environmental epidemiologic studies to detect spatial clustering of cancer cases in a geographic area of interest.

The TP53 database compiles various types of data and information from the literature and generalist databases on human TP53 gene variations related to cancer.

Cancer Imaging Program (CIP) Investigational New Drug (IND) Directory is a centralized resource to facilitate the sharing of IND information.