TCI-BCI members produce other scientific products:
Statistical Software Packages and Apps
R Packages
R packages for detecting adverse events
- Diniz MA. EWOC: Escalation With Overdose Control. R package version 0.3.0
- Diniz MA. visae: Visualization of Adverse Events. R package version 0.1.0
R packages for control of multiple comparison
- Diniz MA, Gallardo D, Magalhaes TM. MCPModBC: Improved Inference in Multiple Comparison Procedure – Modelling
R packages for the differential co-expression (or co-abundance) network analysis
R packages for quantile regression
- Song X, WEE (A weighted estimating equation based method for secondary analysis in case control studies)
- Song X, QRank (Quantile regression tool for eQTL discovery)
R packages for integrative -omic data analysis
- Song X, MiXcan (cell-type-aware transcriptome-wide association analysis)
- Song X, iProMix( cell-type specific association analysis
- Song X, iProFun (integrating multi-omics data to identify function consequences of DNA alterations)
- Song X, ProTrack (Interactive web tool to visualize multi-omic data)
- Song X, CPTACdream (Package of NCI-CPTAC DREAM Proteogenomics Challenge to predict protein levels from copy number and transcrpit levels and phosphorylation levels from protein levels.)
Statistical Applications and Tools
Kwon D, Reddy RRS, Reis IM. ABCMETAapp: R shiny application for simulation-based estimation of mean and standard deviation for meta-analysis via approximate Bayesian computation.
Joshi H, Jain M, Van Hyfte G. Sample Size Calculator for Selection Trials Using Equivalence Designs in Phase II Studies.
Pedraza AM, Parekh S, Joshi H, Grauer R, Wagaskar V, Zuluaga L, Gupta R, Barthe F, Nasri J, Pandav K, Patel D, Gorin MA, Menon M, Tewari AK. Side-specific, Microultrasound-based Nomogram for the Prediction of Extracapsular Extension in Prostate Cancer. Eur Urol Open Sci. 2022 Dec 28;48:72-81. doi: 10.1016/j.euros.2022.12.005. PMID: 36743400; PMCID: PMC9895764.
Textbooks and Book Chapters
Clinical Trial Design
Diniz MA, de Bragança Pereira CA, Polpo A. Bayesian semiparametric symmetric models for binary data. Interdisciplinary Bayesian Statistics. Springer International Publishing, 2015. 323-335 https://doi.org/10.1007/978-3-319-12454-4_27
Magalhães TM, Diniz MA. Normality: Assumptions, Transformations and Outliers. In: Lunardi C Adriana (eds) Manual of Clinical Research Applied to Health. Blucher, 2020. 349-364
Diniz, M.A., Magalhães, T.M. (2020). Logistic Regression and Related Methods. In: Piantadosi, S., Meinert, C. (eds) Principles and Practice of Clinical Trials. Springer, Cham. https://doi.org/10.1007/978-3-319-52677-5_122-2
Jiménez JL, Diniz MA, Rogatko A, Tighiouart M. Designs of Early Phase Cancer Trials with Drug Combinations. In: Modern Statistical Methods for Health Research. Springer, Cham. 2021. 131-160. https://doi.org/10.1093/annonc/mdu516
Mazumdar, M., Zhong, X., Ferket, B. (2021). Diagnostic Trials. In: Piantadosi, S., Meinert, C.L. (eds) Principles and Practice of Clinical Trials. Springer, Cham. https://doi.org/10.1007/978-3-319-52677-5_281-1
-Omics Data Analysis
Song, Xiaoyu. “Statistical and Computational Methods for Proteogenomic Data Analysis.” In Statistical Genomics, pp. 271-303. New York, NY: Springer US, 2023. https://doi.org/10.1007/978-1-0716-2986-4_13
Edited Books
Bang H, Zhou XK, Epps HL, Madhu Mazumdar (Eds.) (2010) Statistical Methods in Molecular Biology. Humana Totowa, NJ