Web Application Registry

Members of the Department of Biostatistics and the Center for Quantitative Sciences have developed or participated in the development of web applications. These applications have their own uses and can also serve as inspiration for the development of new applications.

If you have participated in the building of a web application and would like it listed here then edit this topic to include your work or send an email to dale.plummer@vanderbilt.edu. We would like to have the name of the application, a link, the technology used (e.g. PHP, Python, rApache, Rook, etc.), and a short description of the application's function.

Title Description Author Technology
Nonbipartite Matching See link Robert Greevy and Cole Beck  
Reweighted Mahalanobis Distance Matching in Observational Studies and Randomized Trials See link Robert Greevy and Cole Beck  
MortCalc A Mortgage Calculator Matt Shotwell yarr (my own R package implementation of brew-like functionality), rApache
RefiCalc A Mortgage Refinance Calculator Matt Shotwell yarr, rApache
A calculator for the number of adverse events that could be prevented with a preemptive genotyping program See link Jonathan Schildcrout R and Rapache
Calculates normal ranges for ECG parameters based on user inputs See link Jonathan Schildcrout (Dana Blakemore did most of development) R and Rapache
Dotplot This application plots the data in a way individual data are visible. As an option a boxplot may be overlaid. Tatsuki Koyama and Will Gray R Brew
3+3 phase I clinical trial design This application computes probabilities and expected sample sizes of a typical "3+3" design for a phase I clinical trial. Tatsuki Koyama R Brew
Bivariate baseball score plot This application plots scores from major league baseball (1884 to 2007). We need to update the data... Tatsuki Koyama R Brew
Proper inference from Simon's two-stage designs This application computes p-value, an estimate with a confidence interval of a response probability from a Simon's two-stage design. Tatsuki Koyama and Will Gray R Brew
WebGestalt WebGestalt is a "WEB-based GEne SeT AnaLysis Toolkit". It is designed for functional genomic, proteomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides an easy way for biologists to make sense out of gene lists. Developed and maintained in the Zhang lab by Jing Wang (DBMI), Dexter Duncan (Biostatistics), Bing Zhang (DBMI). The project was initiated by Bing Zhang, Stefan Kirov, Denise Schmoyer, and Jay Snoddy in 2003 PHP, Perl, R, HTML, CSS, information from several public databases including NCBI, Gene Ontology, KEGG, Wikipathways and Wikipathways API, International Protein Index, Pathway Commons, MGI, SGD, MSigDB, Local (In House) Network Computation Analysis, Affymetrix, Illumina, Ensembl
Canprovar CanProVar is designed to store and display single amino acid alterations including both germline and somatic variations in the human proteome, especially those related to the genesis or development of human cancer based on the published literatures. Cancer-related variations and corresponding annotations can be queried through the web-interface using Protein IDs in the Ensembl, IPI, RefSeq, and Uniport/Swiss-Prot databases or gene names and Entrez gene IDs. Fasta files with variation information are also available for download. Developed and maintained in the Zhang lab by Dexter Duncan (Biostatistics) and Bing Zhang (DBMI) in the Zhang Lab. The project was initiated by Jing Li and Bing Zhang in 2009 PHP, CSS, HTML, MySQL, information from public databases and literature
GLAD4U The goal of Gene List Automatically Derived For You (GLAD4U) is to implement an algorithm searching the scientific literature (Pubmed) to retrieve the list of publications corresponding to a user’s query. The algorithm will then translate the list of publications into a list of genes referenced in these publications. The last step is to present the user with the list of prioritized genes, from the most to the least referenced genes within the search space. This application computes p-value, an estimate with a confidence interval of a response probability from a Simon's two-stage design. Developed in the Zhang lab by Jerome Jourquin (DBMI), Dexter Duncan (Biostatistics) and Bing Zhang (DBMI) PHP, CSS, HTML, C, R, NCBI E-utilities eSearch
BIGCAT/ATP BIGCAT is an integrated suite of browser-driven, multi-functional analysis software for interpreting, comparing, and displaying tandem mass spectrometry results. BIGCAT relies on a back-end Oracle database utilizing a simple, adaptable schema for results storage. Interactive, web-deployed front-end applications allows users to filter, view, compare, analyze, and visualize mass spectrometry results. Developed in the laboratory of Andrew Link by Michael Assink (VICTR), Dexter T. Duncan (Biostatistics), K. Jill McAfee (Office of Research), and Xinnan Niu (Microbioloy and Immunology)

PHP, HTML, CSS, Oracle

Hmisc Power and Sample Size Calculator (source code). Using the spower function from Hmisc, along with related plot functions, this calculator simulates a 2-arm, 5-year follow-up study using Hmisc. All subjects are followed at least one year, and patients enter the study with linearly increasing probability starting with zero. Assume (1) there is no chance of drop in for the first 6 months, then the probability increases linearly up to .15 at 5 years; and (2) there is a linearly increasing chance of dropout up to .3 at 5 years. Frank Harrell, Jeffrey Horner Shiny
VPE (source code) A Web Application for Verification of Pathogen Eradication (AVPE) in Animal Colonies. An aid for determining when an infected animal colony can return to normal operations William Dupont, Dale Plummer Shiny
Likelihood Ratio Statistics for 2X2 Tables This calculator provides p-values based on the profile and conditional likelihood ratio (LR) statistics for 2 x 2 tables Leena Choi, Jeffrey D. Blume, William D. Dupont Shiny
Visual Pruner Visual Pruner is a study-design tool for use with observational studies Lauren R. Samuels and Robert A. Greevy, Jr. Shiny
Topic revision: r9 - 23 Dec 2015, DalePlummer

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