Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

Combine generalised least squares methodology from the nlme package for dealing with autocorrelation with penalised least squares methods from the glmnet package to deal with high dimensionality. This pengls packages glues them together through an iterative loop. The resulting method is applicable to high dimensional datasets that exhibit autocorrelation, such as spatial or temporal data.

Platform Design Info for The Manufacturer's Name HG_U95B.

This package provides a GUI interface for the DAPAR package. The package Prostar (Proteomics statistical analysis with R) is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required.

Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements.

Package for the position related analysis of quantitative functional genomics data.

Platform Design Info for Affymetrix RaGene-2_1-st.

Platform Design Info for Affymetrix MTA-1_0.

Platform Design Info for Affymetrix CynGene-1_0-st.

Platform Design Info for The Manufacturer's Name RG_U34C.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was P\_aeg1a\_probe\_tab.

Platform Design Info for The Manufacturer's Name Rhesus.

Platform Design Info for The Manufacturer's Name HG-U133_Plus_2.

Platform Design Info for The Manufacturer's Name Poplar.

Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.

Platform Design Info for Affymetrix MoGene-2_1-st.

This package provides a Bioconductor data package for the Stockholm dataset.

peakCombiner, a fully R based, user-friendly, transparent, and customizable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimize input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses.

Platform Design Info for NimbleGen feinberg_hg18_me_hx1.

PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs.

Platform Design Info for Affymetrix FinGene-1_0-st.

Platform Design Info for Affymetrix CanGene-1_0-st.

Platform Design Info for The Manufacturer's Name Rat230_2.

Platform Design Info for Affymetrix RCnGene-1_1-st.