Pharmacogenomic software tools | Drug discovery data analysis
Pharmacogenetics, one of the cornerstones of personalized medicine, has the potential to change the way in which health care is offered by stratifying patients into various pretreatment categories, such as likely responders, likely non-responders or likely to experience adverse drug reactions.
Allows a facile amino-acid focused downstream analysis. SNP2HLA is a software which imputes amino acid polymorphisms and single nucleotide polymorphisms (SNPs) in human leukocyte antigenes (HLA) within the major histocompatibility complex (MHC) region in chromosome 6. It also provides a companion package, MakeReference, which software builds the reference panel that can be used for SNP2HLA.
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.
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).
An R package enabling users to download and interrogate large pharmacogenomic datasets that were extensively curated to ensure maximum overlap and consistency. PharmacoGx provides parallelized functions not only to assess the reproducibility of pharmacological and molecular data, but also to identify the molecular features that are consistently associated with drug effects.
Predicts many kinds of biological activity for compounds from different chemical series based on their 2D structural formulas. PASS finds new targets mechanisms for some ligands. It can reveal new ligands for some biological targets. The tool can be used to analyze the occurrence, in a database, of compounds predicted to be active for a well-defined set of PASS activities.