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Platform Design Info for Affymetrix RUSGene-1_1-st.
Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1.
Pviz adapts the Gviz package for protein sequences and data.
Platform Design Info for Affymetrix RUSGene-1_0-st.
Platform Design Info for The Manufacturer's Name HG-U219.
Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.
Platform Design Info for Affymetrix CanGene-1_1-st.
Platform Design Info for Affymetrix HTA-2_0.
Platform Design Info for The Manufacturer's Name Mouse430A_2.
This package provides a package containing an environment representing the PrimeView.cdf file.
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 miRNA-1_0.
Platform Design Info for Affymetrix CynGene-1_1-st.
Platform Design Info for Affymetrix miRNA-3_1.
Platform Design Info for The Manufacturer's Name RAE230A.
Platform Design Info for The Manufacturer's Name Rat230_2.
Platform Design Info for The Manufacturer's Name MG_U74C.
This package provides tools for large-scale protein motif analysis and visualization in R. PMScanR facilitates the identification of motifs using external tools like PROSITE's ps_scan (handling necessary file downloads and execution) and enables downstream analysis of results. Key features include parsing scan outputs, converting formats (e.g., to GFF-like structures), generating motif occurrence matrices, and creating informative visualizations such as heatmaps, sequence logos (via seqLogo/ggseqlogo). The package also offers an optional Shiny-based graphical user interface for interactive analysis, aiming to streamline the process of exploring motif patterns across multiple protein sequences.
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.
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.
Platform Design Info for Affymetrix FinGene-1_0-st.
Platform Design Info for Affymetrix CHOGene-2_1-st.
Platform Design Info for The Manufacturer's Name Bovine.
Platform Design Info for Affymetrix RaEx-1_0-st-v1.