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

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

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

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 Affymetrix GenomeWideSNP_5.

Peptide Set Test (PepSetTest) is a peptide-centric strategy to infer differentially expressed proteins in LC-MS/MS proteomics data. This test detects coordinated changes in the expression of peptides originating from the same protein and compares these changes against the rest of the peptidome. Compared to traditional aggregation-based approaches, the peptide set test demonstrates improved statistical power, yet controlling the Type I error rate correctly in most cases. This test can be valuable for discovering novel biomarkers and prioritizing drug targets, especially when the direct application of statistical analysis to protein data fails to provide substantial insights.

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

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was PrimeView\_probe\_tab.

Platform Design Info for The Manufacturer's Name Tomato.

Platform Design Info for The Manufacturer's Name Zebrafish.

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

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 uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH).

Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.

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

This package provides a shiny app-based GUI wrapper for ggplot with built-in statistical analysis. Import data from file and use dropdown menus and checkboxes to specify the plotting variables, graph type, and look of your plots. Once created, plots can be saved independently or stored in a report that can be saved as a pdf. If new data are added to the file, the report can be refreshed to include new data. Statistical tests can be selected and added to the graphs. Analysis of flow cytometry data is especially integrated with plotGrouper. Count data can be transformed to return the absolute number of cells in a sample (this feature requires inclusion of the number of beads per sample and information about any dilution performed).

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

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

Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.

Platform Design Info for The Manufacturer's Name ATH1-121501.

Platform Design Info for The Manufacturer's Name Mu11KsubB.

Platform Design Info for NimbleGen feinberg_hg18_me_hx1.

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

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Plasmodium\_Anopheles\_probe\_tab.