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Enables researchers to perform classical Human Leukocyte Antigen (HLA) allele imputation. HLA*IMP is a framework for classical HLA types, based on a parallelized model-building algorithm and a large set of carefully assembled training data. HLA allele imputation are calculated from genotype data collected from several available genome-wide single nucleotide polymorphism (SNP) sets through reference to a reference dataset of over 2500 samples of European ancestry with dense SNP data and classical HLA allele types.
Provides a core resource for the bio-defense and infectious disease research community. Pathema is a web application that permits the access to genomic data integrated with analysis tools designed to aid researchers in identifying potential targets for novel therapeutics, vaccines, and diagnostics. The priority pathogens support includes five prokaryotes (Bacillus anthracis, Burkholderia mallei, Burkholderia pseudomallei, Clostridium botulinum and Clostridium perfringens) and one eukaryote (Entamoeba histolytica).
Provides a wide range of functionality to help R users access and explore molecular profiling and drug response data for the NCI-60. The package enables flexible programmatic access to CellMiner's unparalleled breadth of NCI-60 data, including gene and protein expression, copy number, whole exome mutations, as well as activity data for ~21K compounds, with information on their structure, mechanism of action, and repeat screens. Functions are available to easily visualize compound structures, activity patterns, and molecular feature profiles. Additionally, embedded R Shiny applications allow interactive data exploration.
CellMiner Companion
A web application that enables researchers to explore the output of CellMiner queries. The data from multiple files is summarized, assembled into a single data matrix, z-score normalized, clustered, and visualized both as a heatmap and dendrogram. Users can interactively change many parameters to explore the relationship among drugs or genes across the NCI-60 cell lines. Importantly, this tool increases the accessibility of the NCI-60 data to those lacking programming skills.
A repository to house the code relevant to the project "Systematic Rational Identification of Sex-Linked Molecular Alterations and Therapies in Cancer." The repository contains R scripts used to process and analyze data and results. In our work, we identify cancer-specific and pan-cancer genomic differences between male and female patients. Then, we use Ingenuity Pathway Analysis (IPA) to discover pathways variably enriched in male and female tumors, lending insight into the biological processes that differ between both sexes. Finally, we use our genomic findings to identify drugs that work well in males, females, or both sexes.
HIBAG / HLA Genotype Imputation with Attribute Bagging
Imputes HLA types using single-nucleotide polymorphism (SNP) data. HIBAG is a software package which combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and human leukocyte antigen (HLA) types. The package includes pre-fit classifiers for European, Asian, Hispanic and African ancestries, providing a readily available imputation approach without the need to have access to large training data sets.
Detects spurious attributed human leukocyte antigen (HLA) alleles. HLA-check relies the precise Single Nucleotide Polymorphism (SNP) imputation in the exonic parts of HLA genes currently using the 1000 genome reference panel. The use of HLA-check could remove a small proportion of individuals, but could allow a higher accuracy in association detection justifying its use for research purposes. It performs very quickly (on a personal computer): only a few seconds per tested individual are needed to obtain the final comparison value for a given HLA.
Predicts complex traits. OmicKriging leverages and integrates similarity in genetic, transcriptomic, and/or other large scale omics data. It emphasizes the use of a wide variety of systems-level data. The tool is able to integrate other sources of information such as prior evidence of association or function and even geographic proximity. It generates correlation matrices from single nucleotide polymorphism (SNP), gene expression, methylation or other 'omics' datasets and predicts the phenotype of an individual by using the phenotypes of the remaining individuals through kriging.
Identifies pharmacogenomic facts in full text articles. Pharmspresso is a text mining tool that extracts information from full text articles by identifying key pharmacogenomic concepts and the relationships between them. The software can process full text articles and index their contents based on an ontology of key concepts, on a corpus of literature relevant to the field of pharmacogenomics. Its corpus consists in papers from the PharmGKB, which have been manually verified as relevant to pharmacogenomics.
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