Software and Tools
The Division of Cancer Treatment and Diagnosis (DCTD) develops software and tools for the benefit of the scientific community.
The applications included in this page are developed and maintained by researchers and staff within the Biometric Research Program.
The applications are free for non-commercial use and offered "as-is". Users who download the software agree not to use any trademarks, service marks, trade names, logos, or product names of NCI or NIH to endorse or promote products derived from the applications without specific, prior, and written permission. Additional terms of use are included in license agreements distributed with each application.
Available Software Tools
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tmbLab
Tumor mutational burden (TMB) calibration tool. The software estimates a calibration curve with corresponding prediction limits to quantify the average relationship between whole exome sequencing (WES) and panel TMB assay values.
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MutSpliceDB
Database of splice sites variants. MutSpliceDB documents mutation effects on splicing (e.g., exon inclusion/exclusion or intron retention) based on RNA-seq BAM files from samples with particular splice site mutations.
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TPWshiny
TPWshiny provides dynamic visualization for data in the NCI Transcriptional Pharmacodynamics Workbench (NCI TPW), a genome-wide characterization of NCI-60 human cell lines in response to 15 anticancer drugs.
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NCI Transcriptional Pharmacodynamics Workbench
The NCI Transcriptional Pharmacodynamics Workbench (NCI TPWB) provides scientists access to the genome-wide characterization of the NCI-60 cell lines and the enormous time-course databases on genome-wide response to treatment with drugs.
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BRB-ArrayTools
BRB-ArrayTools is a tool for the visualization and statistical analysis of Microarray gene expression, copy number, methylation and RNA-Seq data. It is distributed as set of modularized R Packages or Excel add-on.
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D3Oncoprint
Standalone software to dynamically explore annotated genomic mutation files. The focus on interactive visualization with sample annotation empowers researchers to translate information from the data into biological insights and clinical applications.
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OpenGeneMed
An open and customizable version of the GeneMed system (Zhao et al, 2015), a web-based interface developed for the Molecular Profiling based Assignment of Cancer Therapy (NCI-MPACT) clinical trial coordinated by the NIH.
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Accelerated Titration Design Software
A design for Phase I trial that is safe, reduces the number of patients treated at sub-therapeutic dose levels, reduces the duration of the trial and provides more information on toxicity data.
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Optimal Two-Stage Phase II Design Software
Easy to use, compiled C program computing optimal and minimax two-stage designs for phase II clinical trials.
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pCR Trial-Level Surrogate Analysis Software
R package with code, data, and results of the analysis reported in the published paper "Assessing pathological complete response as a trial-level surrogate endpoint for early-stage breast cancer" (Korn, Sachs, and McShane, Ann Oncol 27, 2016).
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Online Sample Size Calculation
A group of online sample size calculators for different clinical trials design strategies and approaches.