AMP PD offers multiple types of content and tools that are available to researchers. External to the Portal and Terra are “explorer & visualization tools,” that are developed as supplemental resources to Terra and can be used as stand-alone applications for sophisticated analysis. Researchers can use these tools to analyze AMP PD clinical, transcriptomics, and genomics data and/or in-conjunction with disparate datasets.
These tools make it easier for researchers to run canned queries and visualize results in a targeted fashion. Access to these external tools requires approval, authentication, and user login.
The Data Explorer tool allows users the ability to create and save cohorts and sets of samples by choosing the subsets of data that are relevant to their research. Saved cohorts and sets can be exported to a workspace for further analysis.
The Gene Analysis Toolkit (GATK) offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Parallel coordinates is an interactive tool for data analysis and exploration. It is specifically designed to display data sets with many variables, enabling the researcher to discover interesting relationships between those variables.
GenoML is an Automated Machine Learning (ML) tool that optimizes basic machine learning pipelines for genomic data. GenoML will automate the most tedious part of ML by intelligently exploring many possible models to find the best one for your data.
The RNA-Seq Data Explorer App provides access to gene-level RNA-seq data, quality metrics, and integration with previous DNA-based studies. Users can explore cohorts & quality, browse genomes, and perform gene-level plotting.
Bravo Variant Tool
Shows chromosome locations, VEP functional annotations, and allele frequencies. The sequencing analysis pipeline consists of two major processes: Data harmonization from BAM files and Joint variant discovery & genotype calling across studies.