Bioconductor
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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 ⋮ Clustering with the average silhouette width ⋮ Bayesian regularization of Gaussian graphical models with measurement error ⋮ More powerful tests for sparse high-dimensional covariances matrices ⋮ Data mining techniques for the life sciences ⋮ Statistical genomics. Methods and protocols ⋮ Fluctuation domains in adaptive evolution ⋮ Identifying intergenerational patterns of correlated methylation sites ⋮ Bayesian analysis of RNA-Seq data using a family of negative binomial models ⋮ Book review of: R. Gentleman et al., Bioinformatics and computational biology solutions using R and bioconductor ⋮ HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test ⋮ A Markov random field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data ⋮ Comparing five statistical methods of differential methylation identification using bisulfite sequencing data ⋮ Shrinkage of dispersion parameters in the binomial family, with application to differential exon skipping ⋮ Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression ⋮ A practical guide to big data ⋮ Advances in integrative statistics for logic programming ⋮ Ergodicity of combocontinuous adaptive MCMC algorithms ⋮ On hyperbolic transformations to normality ⋮ Ridge estimation of inverse covariance matrices from high-dimensional data ⋮ Nested nonnegative cone analysis ⋮ Modifying SAMseq to account for asymmetry in the distribution of effect sizes when identifying differentially expressed genes ⋮ Bayesian estimation of differential transcript usage from RNA-seq data ⋮ The potential and perils of preprocessing: building new foundations ⋮ A statistical method for measuring activation of gene regulatory networks ⋮ Bayesian mixed effects models for zero-inflated compositions in microbiome data analysis ⋮ An iterative algorithm for fitting nonconvex penalized generalized linear models with grouped predictors ⋮ Correlation tests for high-dimensional data using extended cross-data-matrix methodology ⋮ Integrative correlation: properties and relation to canonical correlations ⋮ Inference on high-dimensional mean vectors with fewer observations than the dimension ⋮ A hybrid algorithm for the DNA sequencing problem ⋮ Bioinformatics. Volume II: structure, function, and applications ⋮ Inferring metabolic networks using the Bayesian adaptive graphical Lasso with informative priors ⋮ A systems biology approach to understanding alcoholic liver disease molecular mechanism: the development of static and dynamic models ⋮ Extending lattice: using generics and methods to implement new visualization methods within the Trellis framework ⋮ 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 ⋮ 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 ⋮ Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis ⋮ Node sampling for protein complex estimation in bait-prey graphs ⋮ Laplace approximated EM microarray analysis: an empirical Bayes approach for comparative microarray experiments ⋮ Adaptive Gibbs samplers and related MCMC methods ⋮ Multiple hypothesis testing and clustering with mixtures of non-central \(t\)-distributions applied in microarray data analysis ⋮ Pathway-based kernel boosting for the analysis of genome-wide association studies ⋮ Computational exposition of multistable rhythms in 4-cell neural circuits ⋮ An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies ⋮ Deriving and comparing the distribution for the number of false positives in single step methods to control \(k\)-FWER ⋮ Boosting algorithms: regularization, prediction and model fitting ⋮ Rejoinder: Boosting algorithms: regularization, prediction and model fitting ⋮ MATHT: a web server for comprehensive transcriptome data analysis ⋮ Strong approximations of level exceedences related to multiple hypothesis testing ⋮ Modeling read counts for CNV detection in exome sequencing data ⋮ Incorporating biological information into linear models: a Bayesian approach to the selection of pathways and genes ⋮ Computational cell biology. Methods and protocols ⋮ The class of microarray games and the relevance index for genes ⋮ On computing maximum likelihood estimates for the negative binomial distribution ⋮ Bayesian factor models for the detection of coherent patterns in gene expression data ⋮ Meta-analysis for ranked discovery datasets: theoretical framework and empirical demonstration for microarrays ⋮ Comparing segmentation methods for genome annotation based on RNA-seq data ⋮ Estimation and testing of gene expression heterosis ⋮ A look at multiplicity through misclassification ⋮ A multivariate version of the Benjamini-Hochberg method ⋮ Controlling the false-discovery rate by procedures adapted to the length bias of RNA-seq ⋮ Anesthetic propofol-induced gene expression changes in patients undergoing coronary artery bypass graft surgery based on dynamical differential coexpression network analysis ⋮ A simulation framework for correlated count data of features subsets in high-throughput sequencing or proteomics experiments ⋮ Finite mixtures of skew Laplace normal distributions with random skewness ⋮ Sample size calculation based on generalized linear models for differential expression analysis in RNA-seq data ⋮ Efficient design and analysis of two colour factorial microarray experiments ⋮ Linear latent variable models: the lava-package ⋮ Distribution modeling and simulation of gene expression data ⋮ Modified linear discriminant analysis approaches for classification of high-dimensional microarray data ⋮ Exploration of distributional models for a novel intensity-dependent normalization procedure in censored gene expression data ⋮ Interacting with local and remote data repositories using the stashR package ⋮ Caching code chunks in dynamic documents. The weaver package ⋮ JavaStat: a Java/R-based statistical computing environment ⋮ Modeling microbial abundances and dysbiosis with beta-binomial regression ⋮ Gaga: a parsimonious and flexible model for differential expression analysis ⋮ A cross-validation based estimation of the proportion of true null hypotheses ⋮ Dynamical properties of feedback signalling in B lymphopoiesis: a mathematical modelling approach ⋮ Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis ⋮ Projection Pursuit Based on Gaussian Mixtures and Evolutionary Algorithms ⋮ Algebraic and topological indices of molecular pathway networks in human cancers ⋮ Flexible mixture modeling via the multivariate \(t\) distribution with the Box-Cox transformation: an alternative to the skew-\(t\) distribution ⋮ Maximum likelihood inference for mixtures of skew Student-\(t\)-normal distributions through practical EM-type algorithms ⋮ On-line changepoint detection and parameter estimation with application to genomic data ⋮ HmmSeq: a hidden Markov model for detecting differentially expressed genes from RNA-seq data ⋮ Empirical characterization of random forest variable importance measures ⋮ The analysis of gene expression data. Methods and software ⋮ Classification and clustering of sequencing data using a Poisson model ⋮ 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 ⋮ A statistical perspective on the challenges in molecular microbial biology ⋮ An efficient and flexible multiplicity adjustment for chi-square endpoints ⋮ Four papers on contemporary software design strategies for statistical methodologists ⋮ Object-oriented programming, functional programming and \texttt{R} ⋮ Scalable genomics with \texttt{R} and bioconductor
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