Bioconductor

swMATH4205MaRDI QIDQ16389FDOQ16389

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Described by source

• Bioinformatics and computational biology solutions using R and Bioconductor.
• Statistics and data analysis for microarrays using R and Bioconductor. With CD-ROM.

Cited In (only showing first 100 items - show all)

• On computing maximum likelihood estimates for the negative binomial distribution
• Test-statistic correlation and data-row correlation
• A semi-parametric Bayesian approach for detection of gene expression heterosis with RNA-seq data
• Identifying atypically expressed chromosome regions using RNA-Seq data
• Computational cell biology. Methods and protocols
• Refining cellular pathway models using an ensemble of heterogeneous data sources
• Robust estimation of the parameters of \(g\)-\textit{and}-\(h\) distributions, with applications to outlier detection
• An empirical Bayes change-point model for transcriptome time-course data
• Significance tests to identify regulated proteins based on a large number of small samples
• Dynamic adaptive procedures that control the false discovery rate
• Confidence distributions and empirical Bayes posterior distributions unified as distributions of evidential support
• A Statistical Framework for Hypothesis Testing in Real Data Comparison Studies
• Identifying intergenerational patterns of correlated methylation sites
• A practical guide to big data
• Dynamical properties of feedback signalling in B lymphopoiesis: a mathematical modelling approach
• Interpoint distance tests for high-dimensional comparison studies
• miRNA–target gene regulatory networks: A Bayesian integrative approach to biomarker selection with application to kidney cancer
• Partial least squares classification for high dimensional data using the PCOUT algorithm
• Projected tests for high-dimensional covariance matrices
• minPtest: a resampling based gene region-level testing procedure for genetic case-control studies
• RNA bioinformatics
• HDBRR: a statistical package for high-dimensional Bayesian ridge regression without MCMC
• Model-based feature selection and clustering of RNA-seq data for unsupervised subtype discovery
• Nested nonnegative cone analysis
• A mixture factor model with applications to microarray data
• Context-Specific Nested Effects Models
• Modifying SAMseq to account for asymmetry in the distribution of effect sizes when identifying differentially expressed genes
• Pathway-based kernel boosting for the analysis of genome-wide association studies
• Inference on high-dimensional mean vectors with fewer observations than the dimension
• A graph Laplacian prior for Bayesian variable selection and grouping
• Modeling cell populations measured by flow cytometry with covariates using sparse mixture of regressions
• A novel matched-pairs feature selection method considering with tumor purity for differential gene expression analyses
• Model simplification for supervised classification of metabolic networks
• Bioinformatics. Volume II: structure, function, and applications
• A systems biology approach to understanding alcoholic liver disease molecular mechanism: the development of static and dynamic models
• Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data
• Neyman's truncation test for two-sample means under high dimensional setting
• RADIOHEAD: radiogenomic analysis incorporating tumor heterogeneity in imaging through densities
• Semi-supervised nonparametric Bayesian modelling of spatial proteomics
• Bayesian mixed effects models for zero-inflated compositions in microbiome data analysis
• A novel individualized drug repositioning approach for predicting personalized candidate drugs for type 1 diabetes mellitus
• \texttt{EBADIMEX}: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples
• Bayesian sparse multivariate regression with asymmetric nonlocal priors for microbiome data analysis
• A statistical perspective on the challenges in molecular microbial biology
• Hierarchical Bayes variable selection and microarray experiments
• Finite mixture modeling using shape mixtures of the skew scale mixtures of normal distributions
• Rotation gene set testing for longitudinal expression data
• Computational exposition of multistable rhythms in 4-cell neural circuits
• Programming with R
• An efficient and flexible multiplicity adjustment for chi-square endpoints
• Pathway analysis for RNA-seq data using a score-based approach
• Adaptive gPCA: a method for structured dimensionality reduction with applications to microbiome data
• A multivariate version of the Benjamini-Hochberg method
• A predictive approach to measuring the strength of statistical evidence for single and multiple comparisons
• On hyperbolic transformations to normality
• Controlling the false-discovery rate by procedures adapted to the length bias of RNA-seq
• Applied Statistical Genetics with R
• Distribution modeling and simulation of gene expression data
• Exploration of distributional models for a novel intensity-dependent normalization procedure in censored gene expression data
• Clustering with the average silhouette width
• Bayesian regularization of Gaussian graphical models with measurement error
• Book review of: R. Gentleman et al., Bioinformatics and computational biology solutions using R and bioconductor
• Graphical modeling for gene set analysis: A critical appraisal
• Predicting \(O\)-glycosylation sites in mammalian proteins by using SVMs
• JavaStat: a Java/R-based statistical computing environment
• Packaging Data Analytical Work Reproducibly Using R (and Friends)
• Functional Regression Analysis of Fluorescence Curves
• BNP-Seq: Bayesian Nonparametric Differential Expression Analysis of Sequencing Count Data
• Including network knowledge into Cox regression models for biomarker signature discovery
• Rejoinder: Boosting algorithms: regularization, prediction and model fitting
• Empirical likelihood tests for nonparametric detection of differential expression from RNA-seq data
• Using GO for statistical analyses
• Modeling read counts for CNV detection in exome sequencing data
• Sample size reassessment for a two-stage design controlling the false discovery rate
• Algebraic and topological indices of molecular pathway networks in human cancers
• A Model-Based Background Adjustment for Oligonucleotide Expression Arrays
• Deriving and comparing the distribution for the number of false positives in single step methods to control \(k\)-FWER
• Interactive Visualization of Hierarchically Structured Data
• Inferring metabolic networks using the Bayesian adaptive graphical Lasso with informative priors
• Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis
• Extending lattice: using generics and methods to implement new visualization methods within the Trellis framework
• The Gibbs-plaid biclustering model
• Detecting differentially expressed genes with RNA-seq data using backward selection to account for the effects of relevant covariates
• Hierarchical modeling and differential expression analysis for RNA-seq experiments with inbred and hybrid genotypes
• Meta-analysis for ranked discovery datasets: theoretical framework and empirical demonstration for microarrays
• Prospects and challenges in R package development
• Fluctuation domains in adaptive evolution
• Bayesian factor models for the detection of coherent patterns in gene expression data
• Bayesian estimation of differential transcript usage from RNA-seq data
• Ergodicity of combocontinuous adaptive MCMC algorithms
• Bayesian analysis of RNA-Seq data using a family of negative binomial models
• Estimation and testing of gene expression heterosis
• The analysis of gene expression data. Methods and software
• Multiclass classification of sarcomas using pathway based feature selection method
• A statistical method for measuring activation of gene regulatory networks
• Finite mixtures of skew Laplace normal distributions with random skewness
• General power and sample size calculations for high-dimensional genomic data
• Parameter estimation for the calibration and variance stabilization of microarray data
• The class of microarray games and the relevance index for genes
• A look at multiplicity through misclassification

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