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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
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
​

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Last modified 8d ago