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Platform Design Info for The Manufacturer's Name E_coli_2.
Platform Design Info for Affymetrix SoyGene-1_0-st.
Platform Design Info for Affymetrix HuGene-2_1-st.
Platform Design Info for Affymetrix Clariom_S_Mouse.
Platform Design Info for Affymetrix miRNA-4_0.
Platform Design Info for The Manufacturer's Name HG-U133B.
This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways.
Protein Group Code Algorithm (PGCA) is a computationally inexpensive algorithm to merge protein summaries from multiple experimental quantitative proteomics data. The algorithm connects two or more groups with overlapping accession numbers. In some cases, pairwise groups are mutually exclusive but they may still be connected by another group (or set of groups) with overlapping accession numbers. Thus, groups created by PGCA from multiple experimental runs (i.e., global groups) are called "connected" groups. These identified global protein groups enable the analysis of quantitative data available for protein groups instead of unique protein identifiers.
This package provides a Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset.
The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.
Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements.
Platform Design Info for The Manufacturer's Name HG_U95E.
Platform Design Info for Affymetrix FelGene-1_0-st.
This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.
This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package.
This package provides functions to Analyze Microarray (Gene Expression) Data.
Platform Design Info for The Manufacturer's Name RN_U34.
Platform Design Info for Affymetrix GenomeWideSNP_5.
Platform Design Info for Affymetrix HuGene-1_1-st-v1.
Platform Design Info for Affymetrix RabGene-1_1-st.
Platform Design Info for Affymetrix Clariom_S_Rat_HT.
Affymetrix Affymetrix Porcine Array annotation data (chip porcine) assembled using data from public repositories.
This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data.
Platform Design Info for Affymetrix GuiGene-1_1-st.