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

Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).

Platform Design Info for The Manufacturer's Name E_coli_2.

Platform Design Info for The Manufacturer's Name HG-U133A.

Platform Design Info for The Manufacturer's Name HG-U133_Plus_2.

Platform Design Info for The Manufacturer's Name Mouse430_2.

Platform Design Info for Affymetrix GuiGene-1_0-st.

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

planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. TFs are identified using pre-built hidden Markov model profiles for DNA-binding domains. Then, auxiliary and forbidden domains are used with DNA-binding domains to classify TFs into families and subfamilies (when applicable). Currently, TFs can be classified in 58 different TF families/subfamilies.

Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.

Platform Design Info for Affymetrix EquGene-1_1-st.

PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.

Platform Design Info for NimbleGen feinberg_mm8_me_hx1.

Platform Design Info for The Manufacturer's Name Canine_2.

Reads files exported from QX Manager or QuantaSoft containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.

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

This package provides a package containing an environment representing the Porcine.cdf file.

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Platform Design Info for Affymetrix RabGene-1_0-st.

Platform Design Info for The Manufacturer's Name Drosophila_2.

Platform Design Info for The Manufacturer's Name MOE430A.

PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs.

Platform Design Info for The Manufacturer's Name HT_HG-U133A.

This package provides a set of annotation maps describing the entire Gene Ontology assembled using data from PANTHER.