Tools library

The Research Analysis Platform provides a full-featured toolkit for preparing and analyzing a wide range of datatypes.

About the Tools Library

The Tools Library under the Tools tab of the platform shows a complete list of apps and workflows available to you. Use filters to quickly find items by name, category, etc.

Learning about Individual Apps

Clicking on the name of an app will open up a separate information page which contains details about the app's inputs, outputs, and other documentation details. For apps encapsulating existing bioinformatics tools this page also contains licensing information, links to the website for that software, and citations to any related publications. This page also shows the version history for the app and developer documentation which describes the inner workings of the app in detail.

Genomics Apps

• Swiss Army Knife app provides access to the following tools

  • BCFtools

  • BEDtools

  • VCFtools

  • vcflib

  • PLINK

  • PLINK2

  • Sambamba

  • SAMtools

  • Picard

  • Tabix

  • Seqtk

  • bgzip

  • bgenix

• FastQC

• Qualimap2

• BWA-MEM

• GATK4 apps

  • Germline Best Practice BAM/CRAM to VCF workflow

  • Base Quality Score recalibrator

  • HaplotypeCaller

  • Single-Sample GenotypeGVCFs genotyper

• CNVkit

• SnpEff

• SnpSift

• Multi-QC

• GLnexus

• OQFE

• Parabricks DeepVariant

• DRAGEN 3.7.8 UKB WGS Germline

Translational Analysis Apps

• Swiss Army Knife app provides access to the following tools

  • PLINK

  • PLINK2

  • PLATO

  • BOLT-LMM

  • REGENIE

  • QCTool

• SAIGE apps

  • Genetic relatedness matrix (GRM) generator

  • Sparse GRM generator

  • Single variant association tester

  • Gene and region based association tester

• PHESANT

• PLINK2 GWAS

• RAREMETAL2

• PRSice-2

• EIGENSOFT

• LocusZoom

• JupyterLab app with PYTHON_R and JupyterLab with Spark Cluster apps provide access to the following R packages

  • BiocManager

  • MendelianRandomization

  • coloc

  • HyPrColoc

  • epiR

  • prevalence

  • incidence

  • outbreak

• JupyterLab with Spark Cluster app provides access to

  • Hail

  • VEP

Statistical Analysis

JupyterLab app and JupyterLab with Spark Cluster app provide access to

• NumPy

• SciPy

• Matplotlib

• Seaborn

• Pandas

JupyterLab app with STATA feature provides access to

• Stata (stata license to be provided by the user)

Image Processing

JupyterLab app with IMAGE_PROCESSING feature provides access to

• nipype

• FreeSurfer

• FSL

JupyterLab app with MONAI_ML feature provides access to

• 3D Slicer (5.8.1)

• monai (1.5.0)

• monailabel (0.8.5)

3D Slicer is an interactive app that provides a 3D Slicer environment for radiology image visualization, registration, segmentation, and advanced analysis.

3D Slicer with MONAI is an interactive app that provides an 3D Slicer environment integrated with MONAI Label for AI-assisted radiology image annotation and analysis. MONAI Label enables intelligent segmentation workflows through pre-trained models and active learning techniques.

Imaging Multitool - MONAI is an app that provides a flexible, GPU-accelerated environment for medical imaging workflows using the MONAI framework. It enables execution of complex medical image analysis tasks without setting up local dependencies or managing computational resources.

ML frameworks

JupyterLab app with ML feature provides access to

• tensorflow

• torch

• cntk

• keras

• scikit-Learn

JupyterLab with Spark Cluster app provides access to

• MLlib

Utility Apps

• URL Fetcher fetches and uploads a file from a remote URL to the platform

• AWS S3 Importer transfers files from S3 bucket to the platform

• ttyd provides a web-based terminal to a platform virtual machine

• Cloud Workstation provides an ssh-accessible workstation

• Table exporter exports a specific entity or the cohort table to CSV

• Dataset Extender ingests a data file and create a new, superset Dataset

• Rebase Cohorts and Dashboards move cohorts from one Dataset to another in your application