National Cancer Institute

NCI Analysis Tools

CCR - Center for Cancer Research

cProSite - Cancer Proteogenomic Data Analysis Site

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.

Methylscape 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.

MicroArray Analysis Pipeline (MAAPster)

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.

Single-cell Atlas in Liver Cancer (scAtlasLC)

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.

CBIIT - CGBB (Computational Genomics & Bioinformatics Branch)

3DVizSNP - Rapid 3D Visualization of SNP Mutations

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!

CGH - Center for Global Health

CC3S - Cervical Cancer Screening Scenario Simulator

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

DCCPS – Division of Cancer Control and Population Sciences

JPSurv

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.

RecurRisk

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.

DCEG – Division of Cancer Epidemiology and Genetics

Age Period Cohort (APC) Web Tool

Age-Period-Cohort 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

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.

Biomarker Tools

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.

Breast Cancer Risk Assessment Tool (BCRAT)

The Breast Cancer Risk Assessment Tool 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.

Colorectal Risk Assessment Tool (CCRAT)

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

ezQTL

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

FORGEdb

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

FORGE2 TF

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.

GWAS Explorer

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 analyses (GWAS).

GWASTarget

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

HPV Visuals

The Human Papillomavirus Visuals (HPV Visuals) website provides visual examples of the natural history/carcinogenic process of HPV infection and progression to precancer, accompanied by relevant clinical data. This platform addresses a significant gap in clinical comprehension of the carcinogenic process and provides exposure to images that are true representations of meaningful changes in the appearance of the cervix that require clinical action.

LDLink

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.

Moles to Melanoma: Recognizing the ABCDE Features

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.

Melanoma Risk Assessment Tool (MRAT)

The Melanoma Risk Assessment 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.

mSigPortal

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.

PIMixture

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.

SOCcer Web Tool

A standardized occupation coding tool for computer-assisted epidemiologic research. To assist epidemiological researchers incorporate 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.

Spatial Power

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.