Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively.

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 Affymetrix HuGene-1_0-st-v1.

This package provides a Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.

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.

Platform Design Info for The Manufacturer's Name Ecoli_ASv2.

Platform Design Info for The Manufacturer's Name Bsubtilis.

This package provides functions to Analyze Microarray (Gene Expression) Data.

Statistical analysis of peptide microarrays.

This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes.

Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 99 vertebrate species.

Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).

Platform Design Info for The Manufacturer's Name Rat230_2.

Platform Design Info for The Manufacturer's Name Celegans.

Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA-seq datasets, we developed a new R package named Pooling RNA-seq and Assembling Models (PRAM), which builds transcript models in intergenic regions from pooled RNA-seq datasets. This package includes functions for defining intergenic regions, extracting and pooling related RNA-seq alignments, predicting, selected, and evaluating transcript models.

This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10.

The complexity of high-throughput quantitative omics experiments often leads to low replicates numbers and many missing values. We implemented a new test to simultaneously consider missing values and quantitative changes, which we combined with well-performing statistical tests for high confidence detection of differentially regulated features. The package contains functions to run the test and to visualize the results.

Platform Design Info for The Manufacturer's Name HG_U95A.

This package contains the function to assess the batch sourcs by fitting all "sources" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book "Batch Effects and Noise in Microarray Experiements, chapter 12.

This package provides a package containing an environment representing the Porcine.cdf file.

Platform Design Info for Affymetrix Clariom_S_Mouse.

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

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

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