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Platform Design Info for Affymetrix GenomeWideSNP_5.
Platform Design Info for Affymetrix MoEx-1_0-st-v1.
This package provides functions to Analyze Microarray (Gene Expression) Data.
Platform Design Info for Affymetrix Clariom_S_Rat.
Platform Design Info for Affymetrix CHOGene-2_1-st.
Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.
Platform Design Info for The Manufacturer's Name Mu11KsubA.
Platform Design Info for The Manufacturer's Name HG-U133A_tag.
PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.
Platform Design Info for The Manufacturer's Name HG_U95E.
Platform Design Info for Affymetrix Clariom_S_Human_HT.
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.
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.
This package contains all the datasets used in the PepsNMR package.
Platform Design Info for The Manufacturer's Name Pae_G1a.
PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.
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.
Platform Design Info for The Manufacturer's Name HT_HG-U133_Plus_PM.
PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE.
Platform Design Info for Affymetrix Clariom_S_Mouse_HT.
This package provides a simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.
Platform Design Info for The Manufacturer's Name miRNA-1_0.
Platform Design Info for The Manufacturer's Name Soybean.
Platform Design Info for The Manufacturer's Name HT_HG-U133A.