Store UCSC phastCons mm39 conservation scores AnnotationHub Resource Metadata. Provide provenance and citation information for UCSC phastCons mm39 conservation score AnnotationHub resources. Illustrate in a vignette how to access those resources.

This package contains all the datasets used in the PepsNMR package.

Platform Design Info for The Manufacturer's Name Yeast_2.

This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.

This package provides a set of annotation maps describing the entire Gene Ontology assembled using data from PANTHER.

This package provides a package for processing protein mass spectrometry data.

Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.

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

The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.

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

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

Platform Design Info for The Manufacturer's Name NuGO_Hs1a520180.

The phenomis package provides methods to perform post-processing (i.e. quality control and normalization) as well as univariate statistical analysis of single and multi-omics data sets. These methods include quality control metrics, signal drift and batch effect correction, intensity transformation, univariate hypothesis testing, but also clustering (as well as annotation of metabolomics data). The data are handled in the standard Bioconductor formats (i.e. SummarizedExperiment and MultiAssayExperiment for single and multi-omics datasets, respectively; the alternative ExpressionSet and MultiDataSet formats are also supported for convenience). As a result, all methods can be readily chained as workflows. The pipeline can be further enriched by multivariate analysis and feature selection, by using the ropls and biosigner packages, which support the same formats. Data can be conveniently imported from and exported to text files. Although the methods were initially targeted to metabolomics data, most of the methods can be applied to other types of omics data (e.g., transcriptomics, proteomics).

Platform Design Info for The Manufacturer's Name MG_U74Bv2.

Platform Design Info for The Manufacturer's Name MG_U74B.

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

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.

ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.

Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.

Platform Design Info for Affymetrix Atdschip_tiling.

This package provides functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.

Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.

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

Platform Design Info for The Manufacturer's Name Vitis_Vinifera.