The package can identify the dysregulated KEGG pathways based on global influence from the internal effect of pathways and crosstalk between pathways.
Confidence intervals for the ratio of locations and for the ratio of scales of two paired samples
Estimation of Linear AR(1) Panel Data Models with Cross-Sectional Heteroskedasticity and/or Correlation
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
Methods for combining independent subset Markov chain Monte Carlo (MCMC) posterior samples to estimate a posterior density given the full data set
RangedSummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012.
Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.
Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al.
A Tool for Identification of Differentially Expressed Pathways using Multi-Statistic Comparison
A Set of Datasets Used in My Classes or in the Book 'Modele Liniowe i Mieszane w R, Wraz z Przykladami w Analizie Danych'
Parallel Analysis for Ordinal and Numeric Data using Polychoric and Pearson Correlations with S3 Classes
Implementing the Coalescent Approach to PCR Simulation Developed by Weiss and Von Haeseler (NAR, 1997)
Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter
Platform Design Info for NimbleGen 2006-10-31_rn34_refseq_promoter
Functions to facilitate power and sensitivity analyses for genetic studies of natural populations
L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model
Implementing Double Bootstrap Linear Regression Confidence Intervals Using the 'perc-cal' Method
Estimating Multiple Gaussian Graphical Models (GGM) in Penalized Gaussian Mixture Models (GMM)
High-Throughput Generation of Genetic Markers and Maps from Molecular Phenotypes for Crosses Between Inbred Strains
Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.
An extension of some of the classes in phylobase. Tree objects now support subnodes on branches
Modelling Competitive Exclusion and Limited Dispersal in a Statistical Phylogeographic Framework
Estimates the parameters of a trading-tree model for the computation of the probability of informed trading
Sequence ('FASTA'), Annotation ('GFF') and Variants ('VCF') for 17 Samples of 'P. Infestans" and 1 'P. Mirabilis'
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Functions for Calculating Dodge Romig, MIL STD 105E and MIL STD 414 Acceptance Sampling Plan
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Creates an envelope that surrounds a set of points plotted in a two dimensional space.
Graphing Nonlinear Relations Among Latent Variables from Structural Equation Mixture Models
Log Linear by Linear Association models and Rasch family models by pseudolikelihood estimation
Piecewise Linear Regression Splines (PLRS) for the association between DNA copy number and gene expression
Parallel Model-Based Clustering using Expectation-Gathering-Maximization Algorithm for Finite Mixture Gaussian Model
Datasets and Functions Featured in Pollock and Edwards R Companion to Essential of Political Analysis
Useful functions for (batch) file conversion and data resampling in microsatellite datasets
A package to estimate posterior probabilities and perform model selection in change-point models using constrained HMM.
web tool for estimating under-five deaths caused by poor-quality antimalarials in sub-Saharan Africa
Kvantitatiivsete meetodite praktikumi asjad / Functions used in the course "Quantitative methods in behavioural sciences" (SHPH.00.004), University of Tartu
Predictive Inference on Totals and Averages of Finite Populations Segmented in Planned and Unplanned Domains.
Classification rule based on Bayesian mixture models with feature selection bias corrected
The package can prioritize candidate disease metabolites based on global functional relationships between metabolites in the context of metabolic pathways
Miscellaneous functions for processing and sample selection of vis-NIR diffuse reflectance data
Transform public proteomics data resources into Bioconductor Data Structures
Penalized Parametric and Semiparametric Bayesian Survival Models with Shrinkage and Grouping Priors
Forecasting of Univariate Time Series Using the Pattern Sequence-Based Forecasting (PSF) Algorithm
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
Performs simulation study to look for publication bias, using a technique described by Ioannidis and Trikalinos; Clin Trials. 2007;4(3):245-53.
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Computes phylogenetic eigenvectors regression (PVR) and phylogenetic signal-representation curve (PSR) (with null and Brownian expectations)