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Platform Design Info for The Manufacturer's Name Poplar.
Affymetrix Affymetrix Porcine Array annotation data (chip porcine) assembled using data from public repositories.
Platform Design Info for NimbleGen charm_hg18_example.
Platform Design Info for The Manufacturer's Name Medicago.
Statistical analysis of peptide microarrays.
Platform Design Info for Affymetrix RCnGene-1_1-st.
Platform Design Info for Affymetrix Clariom_S_Human.
Platform Design Info for Affymetrix miRNA-3_1.
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 Affymetrix EquGene-1_0-st.
PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE.
CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.
Platform Design Info for The Manufacturer's Name Mouse430_2.
PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.
FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories.
Platform Design Info for Affymetrix CynGene-1_0-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 Bsubtilis.
This package provides functions to Analyze Microarray (Gene Expression) Data.
This package provides a package containing an environment representing the Porcine.cdf file.
Platform Design Info for The Manufacturer's Name Plasmodium_Anopheles.
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 The Manufacturer's Name DrosGenome1.
Platform Design Info for The Manufacturer's Name MG_U74B.