Platform Design Info for Affymetrix CHOGene-2_0-st.

Platform Design Info for Affymetrix HuEx-1_0-st-v2.

peakCombiner, a fully R based, user-friendly, transparent, and customizable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimize input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses.

FHCRC Nelson Lab pedbarrayv10 Annotation Data (pedbarrayv10) assembled using data from public repositories.

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 SoyGene-1_0-st.

Platform Design Info for The Manufacturer's Name E_coli_2.

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 PorGene-1_1-st.

pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.

The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.

Platform Design Info for Affymetrix RaGene-1_0-st-v1.

Platform Design Info for The Manufacturer's Name HG_U95Av2.

Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 99 vertebrate species.

This package provides a toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.

Platform Design Info for The Manufacturer's Name Pae_G1a.

This package provides a package containing an environment representing the Pae_G1a.CDF file.

This package provides a comprehensive set of external and internal evaluation metrics. It includes metrics for assessing partitions or fuzzy partitions derived from clustering results, as well as for evaluating subpopulation identification results within embeddings or graph representations. Additionally, it provides metrics for comparing spatial domain detection results against ground truth labels, and tools for visualizing spatial errors.

Platform Design Info for The Manufacturer's Name X_laevis_2.

Platform Design Info for The Manufacturer's Name MOE430B.

The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.

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.

PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs.

Platform Design Info for The Manufacturer's Name HG-U133B.