Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1.

This package provides a Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset.

PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs.

Platform Design Info for The Manufacturer's Name ATH1-121501.

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.

This package provides a data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples.

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.

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

Platform Design Info for The Manufacturer's Name Xenopus_laevis.

Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

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

Platform Design Info for The Manufacturer's Name RG_U34B.

Platform Design Info for The Manufacturer's Name wheat.

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

Pancreatic ductal adenocarcinoma (PDA) has a relatively poor prognosis and is one of the most lethal cancers. Molecular classification of gene expression profiles holds the potential to identify meaningful subtypes which can inform therapeutic strategy in the clinical setting. The Pancreatic Cancer Adenocarcinoma Tool-Kit (PDATK) provides an S4 class-based interface for performing unsupervised subtype discovery, cross-cohort meta-clustering, gene-expression-based classification, and subsequent survival analysis to identify prognostically useful subtypes in pancreatic cancer and beyond. Two novel methods, Consensus Subtypes in Pancreatic Cancer (CSPC) and Pancreatic Cancer Overall Survival Predictor (PCOSP) are included for consensus-based meta-clustering and overall-survival prediction, respectively. Additionally, four published subtype classifiers and three published prognostic gene signatures are included to allow users to easily recreate published results, apply existing classifiers to new data, and benchmark the relative performance of new methods. The use of existing Bioconductor classes as input to all PDATK classes and methods enables integration with existing Bioconductor datasets, including the 21 pancreatic cancer patient cohorts available in the MetaGxPancreas data package. PDATK has been used to replicate results from Sandhu et al (2019) [https://doi.org/10.1200/cci.18.00102] and an additional paper is in the works using CSPC to validate subtypes from the included published classifiers, both of which use the data available in MetaGxPancreas. The inclusion of subtype centroids and prognostic gene signatures from these and other publications will enable researchers and clinicians to classify novel patient gene expression data, allowing the direct clinical application of the classifiers included in PDATK. Overall, PDATK provides a rich set of tools to identify and validate useful prognostic and molecular subtypes based on gene-expression data, benchmark new classifiers against existing ones, and apply discovered classifiers on novel patient data to inform clinical decision making.

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

Platform Design Info for The Manufacturer's Name Vitis_Vinifera.

Platform Design Info for Affymetrix Clariom_S_Mouse.

Platform Design Info for Affymetrix GenomeWideSNP_6.

Regularization and score distributions for position count matrices.

Platform Design Info for The Manufacturer's Name E_coli_2.

Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC.

Platform Design Info for Affymetrix miRNA-4_0.

Platform Design Info for The Manufacturer's Name Citrus.