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Platform Design Info for The Manufacturer's Name Canine.
This package contains data required to run examples in prebs package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie).
Combine generalised least squares methodology from the nlme package for dealing with autocorrelation with penalised least squares methods from the glmnet package to deal with high dimensionality. This pengls packages glues them together through an iterative loop. The resulting method is applicable to high dimensional datasets that exhibit autocorrelation, such as spatial or temporal data.
Platform Design Info for Affymetrix RheGene-1_1-st.
This package provides a Bioconductor data package for the Stockholm dataset.
Platform Design Info for The Manufacturer's Name ATH1-121501.
Two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile package.
This package provides a data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples.
Platform Design Info for Affymetrix MarGene-1_0-st.
Platform Design Info for The Manufacturer's Name MG_U74Cv2.
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 Zebrafish.
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.
Platform Design Info for Affymetrix FelGene-1_1-st.
Platform Design Info for Affymetrix Atdschip_tiling.
PIPETS provides statistically robust analysis for 3'-seq/term-seq data. It utilizes a sliding window approach to apply a Poisson Distribution test to identify genomic positions with termination read coverage that is significantly higher than the surrounding signal. PIPETS then condenses proximal signal and produces strand specific results that contain all significant termination peaks.
Platform Design Info for Affymetrix Clariom_S_Rat.
Platform Design Info for The Manufacturer's Name Celegans.
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).
This package contains the function to assess the batch sourcs by fitting all "sources" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book "Batch Effects and Noise in Microarray Experiements, chapter 12.
Platform Design Info for Affymetrix CanGene-1_0-st.
FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories.
Platform Design Info for The Manufacturer's Name HG_U95C.
Platform Design Info for The Manufacturer's Name HC_G110.