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

This package provides a Bioconductor data package for the Varambally dataset.

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

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

PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.

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

It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.

Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies.

Pviz adapts the Gviz package for protein sequences and data.

This package provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al.

Platform Design Info for Affymetrix HTA-2_0.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was P\_aeg1a\_probe\_tab.

This package provides a shiny app-based GUI wrapper for ggplot with built-in statistical analysis. Import data from file and use dropdown menus and checkboxes to specify the plotting variables, graph type, and look of your plots. Once created, plots can be saved independently or stored in a report that can be saved as a pdf. If new data are added to the file, the report can be refreshed to include new data. Statistical tests can be selected and added to the graphs. Analysis of flow cytometry data is especially integrated with plotGrouper. Count data can be transformed to return the absolute number of cells in a sample (this feature requires inclusion of the number of beads per sample and information about any dilution performed).

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

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 RabGene-1_0-st.

Platform Design Info for The Manufacturer's Name Bsubtilis.

Platform Design Info for Affymetrix GenomeWideSNP_6.

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

Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.

Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1.

An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.

Platform Design Info for Affymetrix miRNA-3_1.

This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.