Platform Design Info for The Manufacturer's Name Rat230_2.

Platform Design Info for The Manufacturer's Name X_laevis_2.

Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.

Our approach provides a way to assign continuous cell cycle phase using scRNA-seq data, and consequently, allows to identify cyclic trend of gene expression levels along the cell cycle. This package provides method and training data, which includes scRNA-seq data collected from 6 individual cell lines of induced pluripotent stem cells (iPSCs), and also continuous cell cycle phase derived from FUCCI fluorescence imaging data.

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 CanGene-1_0-st.

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

Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.

Platform Design Info for NimbleGen feinberg_hg18_me_hx1.

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

Platform Design Info for Affymetrix RTA-1_0.

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

Platform Design Info for Affymetrix Clariom_S_Mouse.

This package provides a Bioconductor data package for the Grasso (2012) Prostate Cancer dataset.

Platform Design Info for The Manufacturer's Name Citrus.

This package provides a function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.

Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.

Platform Design Info for The Manufacturer's Name Tomato.

Platform Design Info for The Manufacturer's Name RAE230B.

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

Platform Design Info for The Manufacturer's Name Canine_2.

Platform Design Info for The Manufacturer's Name Maize.

FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories.

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