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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.
Relative transcript abundance has proven to be a valuable tool for understanding the function of genes in biological systems. For the differential analysis of transcript abundance using RNA sequencing data, the negative binomial model is by far the most frequently adopted. However, common methods that are based on a negative binomial model are not robust to extreme outliers, which we found to be abundant in public datasets. So far, no rigorous and probabilistic methods for detection of outliers have been developed for RNA sequencing data, leaving the identification mostly to visual inspection. Recent advances in Bayesian computation allow large-scale comparison of observed data against its theoretical distribution given in a statistical model. Here we propose ppcseq, a key quality-control tool for identifying transcripts that include outlier data points in differential expression analysis, which do not follow a negative binomial distribution. Applying ppcseq to analyse several publicly available datasets using popular tools, we show that from 3 to 10 percent of differentially abundant transcripts across algorithms and datasets had statistics inflated by the presence of outliers.
Platform Design Info for The Manufacturer's Name Rhesus.
Platform Design Info for The Manufacturer's Name HG_U95E.
Platform Design Info for Affymetrix GenomeWideSNP_5.
Platform Design Info for Affymetrix HuGene-1_1-st-v1.
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 package provides tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided.
Platform Design Info for The Manufacturer's Name Tomato.
Platform Design Info for The Manufacturer's Name HG-Focus.
Platform Design Info for Affymetrix CHOGene-2_1-st.
Platform Design Info for The Manufacturer's Name Chicken.
Platform Design Info for Affymetrix RCnGene-1_1-st.
Platform Design Info for The Manufacturer's Name Mu11KsubA.
Platform Design Info for Affymetrix FinGene-1_0-st.
This package provides a Bioconductor data package for the Varambally dataset.
Platform Design Info for Affymetrix AraGene-1_0-st.
Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.
The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.
Platform Design Info for Affymetrix CynGene-1_1-st.
This package provides a Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.
Platform Design Info for The Manufacturer's Name HG-U133B.
This package contains all the datasets used in the PepsNMR package.
Platform Design Info for The Manufacturer's Name Citrus.