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Platform Design Info for The Manufacturer's Name HG-Focus.
Platform Design Info for Affymetrix RabGene-1_1-st.
This package provides a package containing an environment representing the PrimeView.cdf file.
Platform Design Info for Affymetrix CyRGene-1_1-st.
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 CanGene-1_1-st.
Platform Design Info for The Manufacturer's Name MOE430B.
This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.
Platform Design Info for Affymetrix DroGene-1_1-st.
Platform Design Info for The Manufacturer's Name Porcine.
Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0).
This package is a gene/phenotype prioritization tool that utilizes multiplex heterogeneous gene phenotype network. PhenoGeneRanker allows multi-layer gene and phenotype networks. It also calculates empirical p-values of gene/phenotype ranking using random stratified sampling of genes/phenotypes based on their connectivity degree in the network. https://dl.acm.org/doi/10.1145/3307339.3342155.
Platform Design Info for Affymetrix EleGene-1_1-st.
Platform Design Info for Affymetrix RaGene-1_0-st-v1.
ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.
Platform Design Info for Affymetrix FinGene-1_1-st.
Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.
This package performs tests for paired high-throughput data.
The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.
Platform Design Info for Affymetrix AraGene-1_0-st.
Platform Design Info for Affymetrix RJpGene-1_1-st.
Platform Design Info for The Manufacturer's Name Hu6800.
This package provides functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.
Platform Design Info for The Manufacturer's Name HC_G110.