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Tools for Anaylsis

BEAGLE

Software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection

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Broad Institute Data, Software and Tools

To find data, software and tools developed by the Broad Institute

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COSMIC Genome Browser

A genome browser for somatic mutations in cancer

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Drug Repurposing Hub

The Repurposing Hub information resource contains extensive curated annotations for each drug, including details about commercial sources of all compounds.

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Drug Bank

A unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information

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GENEASE

Real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization (PMID: 29590301)

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Ensembl

A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation

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Fusion

FUSION is a suite of tools for performing a transcriptome-wide (or any other ome-wide) association study by predicting functional/molecular phenotypes into GWAS using only summary statistics. 

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Galaxy

Galaxy provides the open source and web-based platform with tools necessary to creating and executing variety of analysis pipeline for biomedical research

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Human Metabolome Database

A database containing detailed information about small molecule metabolites found in the human body

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GEO2Enrichr

GEO2Enrichr is a web application and two browser extensions designed to ease the extraction of signatures from studies posted on the Gene Expression Omnibus (GEO) database

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IMPUTE2

Software package that performs genotype imputation and haplotype phasing

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LocusZoom

LocusZoom is a suite of tools to provide fast visualization of GWAS results for research and publication

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LD Hub

A centralised database of summary-level GWAS results and a web interface for LD score regression

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LDlink

A suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups

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McCarthy Tools

This page provides links and information on tools McCarthy group has developed.

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Michigan Imputation server

A server that provides free genotype imputation service

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Sanger Imputation Service

A free genotype imputation and phasing service provided by the Wellcome Trust Sanger Institute

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RNA-Seq Analysis

Galaxy provides the tools necessary to creating and executing a complete RNA-seq analysis pipeline

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SNPnexus

SNP annotation tool

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Stargazer

A bioinformatics tool for calling star alleles of polymorphic pharmacogenes from next-generation sequencing data

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xCell

xCell is a webtool that performs cell type enrichment analysis from gene expression data for 64 immune and stroma cell types. 

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Polygenic Risk Score Variant Weights

Lists of variants and weights comprising polygenic risk scores for five complex diseases, atrial fibrillation, breast cancer, coronary artery disease, inflammatory bowel disease, Type 2 diabetes (PMID: 30104762)

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UCSC Xena

Securely analyze and visualize your private functional genomics data set in the context of public and shared genomic/phenotypic data sets

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CellMinerCDB

Enables exploration and analysis of cancer cell line pharmacogenomic data across different sources.

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PrediXcan

PrediXcan is a gene-based association test that prioritizes genes that are likely to be causal for the phenotype

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SNP2HLA: Imputation of Amino Acid Polymorphisms in Human Leukocyte Antigens

A tool to impute amino acid polymorphisms and single nucleotide polymorphisms in human luekocyte antigenes (HLA) within the major histocompatibility complex (MHC) region in chromosome 6

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PharmCAT

The Pharmacogenomic Clinical Annotation Tool

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