Language: R/Shiny
Repository: BTS
Keywords: Education Statistical Data Analysis
Description: BTS is a web-based R Shiny application for teaching, learning, and performing statistical analyses common in the biological/healthcare sciences.
Language: MATLAB
Repository: coAlign
DOI: 10.1002/cem.3236
Reference(s):
Li Z, Kim S, Zhong S, Zhong Z, Kato I, Zhang X. Coherent Point Drift Peak Alignment Algorithms Using Distance and Similarity Measures for Two-Dimensional Gas Chromatography Mass Spectrometry Data. J Chemom. 2020 Aug;34(8):e3236. doi: 10.1002/cem.3236. Epub 2020 Mar 28. PMID: 33505107; PMCID: PMC7837599.
Deng B, Kim S, Li H, Heath E, Zhang X. Global peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using point matching algorithms. J Bioinform Comput Biol. 2016 Dec;14(6):1650032. doi: 10.1142/S0219720016500323. Epub 2016 Sep 9. PMID: 27650662; PMCID: PMC5226864.
Keywords: Metabolomics Peak Alignment GCxGC-MS Point Matching Algorithm
Description: This is a MATLAB package for global peak alignment on GCxGC-MS Data using point matching algorithms. coAlign can align homogeneous and heterogeneous peaks.
Language: R
Repository: cSILAC
DOI: 10.1016/j.cmpb.2016.09.017
Keywords: Proteomics SILAC PSO Classification
Description: This is an R package for Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) data. cSILAC can do a differential analysis based on PSO-based classification.
Language: MATLAB
Repository: EIder (ComID)
DOI: 10.1016/j.chroma.2016.04.064
Keywords: Metabolomics GC-MS Compound Identification
Description: EIder (EI mass spectrum identifier) provides users with eight literature-reported spectrum matching algorithms for compound identification from gas chromatography mass spectrometry (GC-MS) data.
Language: R
Repository: gen2stage
DOI: 10.29220/CSAM.2019.26.2.163
Keywords: Clinical Trial Design Phase 2 Single-Arm Two-Stage
Description: This is an R package for generalized phase II single-arm two-stage designs for efficacy or toxicity.
Language: R, C
Repository: HTrpart
Keywords: Classification Hypothesis testing Regression trees
Description: Recursively partition a dataset with a continuous or categorical response using the maximum mean rank (continuous outcome) or proportion of any observed class (categorical outcome) as the splitting mechanism to allow for hypothesis testing of each split. The partitioning will stop when there are not more statistically significant splits.
Language: R
Repository: ICAOD
DOI: 10.32614/rj-2022-043
Keywords: Optimal Design Imperialist Competitive Algorithm Nonlinear Models
Description: Finds optimal designs for nonlinear models using a metaheuristic algorithm called Imperialist Competitive Algorithm (ICA).
Language: R
Repository: iFDR
DOI: 10.1002/cem.2665
Keywords: Metabolomics GC-MS Compound Identification Similarity Difference
Description: This is an R package to control FDR in compound identification. iFDR can control the False Identification Rate in compound identification using an empirical Beta model.
Language: R
Repository: iOPT
DOI: 10.1093/bioinformatics/bts083
Keywords: Metabolomics GCxGC-MS Peak Alignment Cosine Similarity
Description: This is an R package for finding optimal weight factors on compound identification. iOPT can find optimal weight factors to obtain more accurate identification.
Language: R
Repository: iPAD
Keywords: Metabolomics GCxGC-MS Peak Alignment Post-Hoc
Description: This is an R package for post-hoc peak alignment on GCxGC-MS Data. iPAD can iteratively align homogeneous peaks based on post-hoc analysis.
Language: R/Shiny
Repository: Mendelian Randomization Analysis
DOI: 10.3390/math10203743
Keywords: Mendelian randomization Extreme phenotype sequencing Causal inference Genome-wide association studies Next generation sequencing studies
Description: This web-based R Shiny application facilitates genetic causal inferences through Mendelian randomization analysis for a one-sample design, based on samples drawn using either a random sampling design or a nonrandom extreme phenotype sequencing design.
Language: R/Shiny
Repository: MRCount
DOI: 10.1002/gepi.22602
Keywords: Mendelian randomization Count data Generalized linear models Genetic causal inferences Instrumental variables
Description: This web-based R Shiny application facilitates genetic causal inferences from count data through Mendelian randomization analysis for a one-sample design.
Language: R
Repository: mSPA
DOI: 10.1093/bioinformatics/btr188
Keywords: Metabolomics GCxGC-MS Peak Alignment
Description: This is an R package for peak alignment on GCxGC-MS Data. mSPA can align homogeneous peaks based on mixture similarity measures.
Language: R
Repository: msPeak
Keywords: Metabolomics GCxGC-MS Peak Detection
Description: This is an R package for peak detection using Bayes factor and mixture probability models. msPeak can do peak detection for GCxGC-MS.
Language: R
Repository: msPeakG
DOI: 10.1016/j.csda.2016.07.015
Keywords: Metabolomics GCxGC-MS Peak Detection
Description: This is an R package for peak detection using Normal-Gamma-Bernoulli models. msPeakG can do peak detection for GCxGC-MS.
Language: Bash; Python
Repository: MZsearch
DOI: 10.26434/chemrxiv-2024-5fm7t
Reference(s):
Hunter Dlugas, Xiang Zhang, Seongho Kim. MZsearch: A Python-Based Compound Identification Tool for GC-MS and LC-MS/MS-Based Metabolomics.
Dlugas, H., Zhang, X., & Kim, S. (2024). Liquid Chromatography - Tandem Mass Spectrometry (LC-MS/MS) and Gas Chromatography - Mass Spectrometry (GC-MS) Reference Libraries from Global Natural Products Social Molecular Networking (GNPS) and National Institute of Standards and Technology (NIST) WebBook Processed for Spectral Library Matching (V1.0) [Data set]. Zenodo.
Dlugas H, Zhang X, Kim S. Comparative analysis of continuous similarity measures for compound identification in mass spectrometry-based metabolomics. ChemRxiv. 2024
Keywords: Compound Identification Metabolomics Similarity Measures
Description: A Python-based tool for spectral library matching, MZsearch is available in two versions: a command-line interface and Python modules for integration into custom code.
Language: Python; R
Repository: NNs_for_binary_classification
Keywords: Artificial Neural Network Bayesian Neural Network Convolutional Neural Network Deep Learning Classification Feedforward Neural Network Kolmogorov-Arnold Network Machine Learning Metabolomics Spiking Neural Network
Description: Implementation of five network-based machine learning models (Bayesian neural networks, convolutional neural networks, feedforward neural networks, Kolmogorov-Arnold networks, and spiking neural networks) to binary classification tasks based on high-dimensional metabolomics data.
Language: R
Repository: ppcor
DOI: 10.5351/CSAM.2015.22.6.665
Reference(s):
Kim S. ppcor: An R Package for a Fast Calculation to Semi-partial Correlation Coefficients. Commun Stat Appl Methods. 2015 Nov;22(6):665-674. doi: 10.5351/CSAM.2015.22.6.665. Epub 2015 Nov 30. PMID: 26688802; PMCID: PMC4681537.
Kim S. P-value calculation methods for semi-partial correlation coefficients. Commun Stat Appl Methods. 2022 May;29(3):397-402. doi: 10.29220/csam.2022.29.3.397. Epub 2022 May 31. PMID: 35756137; PMCID: PMC9230004.
Keywords: Partial Correlation Part Correlation
Description: Calculates partial and semi-partial (part) correlations along with p-value.
Language: R
Repository: PRIMsurvdiff
DOI: 10.23937/2469-5831/1510038
Keywords: Classification PRIM Phase III Subgroup Survival
Description: Use the Patient Rule-Induction Method (PRIM) to identify subgroups of patients based on pre-treatment clinical and demographic characteristics where the experimental treatment is more effective than the standard of care treatment and better than observed in the entire clinical trial cohort with a time-to-event outcome.
Language: R/Shiny
Repository: ShinyMetID
DOI: 10.1016/j.chemolab.2023.104861
Keywords: Compound Identification Metabolomics GC-MS
Description: This is an R/Shiny package for compound identification for GC-MS data.
Language: R
Repository: spatial2stage
DOI: 10.1016/j.csda.2021.107420
Keywords: Clinical Trial Design Phase 2 Single-Arm Two-Stage
Description: This is an R package for spatial two-stage designs for phase II clinical trials.
Language: R/Shiny
Repository: ss2stagePSO
Keywords: Clinical Trial Design Phase 2 Single-Arm Two-Stage PSO
Description: This is an R package for the sample size determination for phase II (middle development) single-arm adaptive two-stage design.
Language: R/Shiny
Repository: ssLogitNorm
Keywords: Clinical Trial Design Power and Sample Size Estimation Logit-Normal
Description: This is an R package for the power and sample size determination on a logit-normal distribution.
Language: R
Repository: swpa2gc
Keywords: Metabolomics Smith-Waterman Peak Alignment
Description: This is an R package for peak alignment on GCxGC-MS Data. SWPA can align homogeneous and heterogeneous peaks based on mixture similarity measures.
Language: R
Repository: time2event
Keywords: Survival Analysis Time-Varing Covariate
Description: Cox proportional hazard and competing risk regression analyses can be performed with time-to-event data as covariates.
* The software tools listed on this page were developed with contributions from one or more members of the Biostatistics and Bioinformatics Core (BBC). Inclusion in this list does not imply ownership, maintenance responsibility, or endorsement by the BBC, KCI, or WSU. All rights and responsibilities remain with the original developers. This listing is intended solely to acknowledge contributions made by BBC members.