Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.

Platform Design Info for Affymetrix RaEx-1_0-st-v1.

Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the field of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge. We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship.

Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.

Platform Design Info for The Manufacturer's Name HG-U133A_tag.

This package provides a function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.

Platform Design Info for The Manufacturer's Name Rat230_2.

Platform Design Info for The Manufacturer's Name NuGO_Mm1a520177.

Platform Design Info for The Manufacturer's Name MG_U74Bv2.

FHCRC Nelson Lab pedbarrayv10 Annotation Data (pedbarrayv10) assembled using data from public repositories.

Platform Design Info for The Manufacturer's Name HG-U133B.

Platform Design Info for The Manufacturer's Name miRNA-1_0.

Platform Design Info for The Manufacturer's Name Xenopus_laevis.

This package provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al.

FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories.

Platform Design Info for The Manufacturer's Name Bsubtilis.

Platform Design Info for The Manufacturer's Name U133_X3P.

Platform Design Info for Affymetrix CHOGene-2_0-st.

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.

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

PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data.

Platform Design Info for The Manufacturer's Name RG_U34B.

Platform Design Info for The Manufacturer's Name Zebrafish.

This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package.