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

This package provides functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.

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

Platform Design Info for The Manufacturer's Name HG-U219.

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 The Manufacturer's Name Mu11KsubA.

Platform Design Info for The Manufacturer's Name RAE230A.

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

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.

preciseTAD provides functions to predict the location of boundaries of topologically associated domains (TADs) and chromatin loops at base-level resolution. As an input, it takes BED-formatted genomic coordinates of domain boundaries detected from low-resolution Hi-C data, and coordinates of high-resolution genomic annotations from ENCODE or other consortia. preciseTAD employs several feature engineering strategies and resampling techniques to address class imbalance, and trains an optimized random forest model for predicting low-resolution domain boundaries. Translated on a base-level, preciseTAD predicts the probability for each base to be a boundary. Density-based clustering and scalable partitioning techniques are used to detect precise boundary regions and summit points. Compared with low-resolution boundaries, preciseTAD boundaries are highly enriched for CTCF, RAD21, SMC3, and ZNF143 signal and more conserved across cell lines. The pre-trained model can accurately predict boundaries in another cell line using CTCF, RAD21, SMC3, and ZNF143 annotation data for this cell line.

Platform Design Info for The Manufacturer's Name Rhesus.

This package provides functions to Analyze Microarray (Gene Expression) Data.

This package provides tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided.

This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.

Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter.

This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes.

The package contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).

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

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

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

The package ptairData contains two raw datasets from Proton-Transfer-Reaction Time-of-Flight mass spectrometer acquisitions (PTR-TOF-MS), in the HDF5 format. One from the exhaled air of two volunteer healthy individuals with three replicates, and one from the cell culture headspace from two mycobacteria species and one control (culture medium only) with two replicates. Those datasets are used in the examples and in the vignette of the ptairMS package (PTR-TOF-MS data pre-processing). There are also used to gererate the ptrSet in the ptairMS data : exhaledPtrset and mycobacteriaSet.

Platform Design Info for Affymetrix MoGene-2_1-st.

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

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.