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Tools Library
The Research Analysis Platform provides a full-featured toolkit for preparing and analyzing a wide range of datatypes.
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.
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.
- BCFtools
- BEDtools
- VCFtools
- vcflib
- PLINK
- PLINK2
- Sambamba
- SAMtools
- Picard
- Tabix
- Seqtk
- bgzip
- bgenix
- GATK4 apps
- Germline Best Practice BAM/CRAM to VCF workflow
- PLINK
- PLINK2
- PLATO
- BOLT-LMM
- REGENIE
- QCTool
- 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
- Hail
- VEP
- NumPy
- SciPy
- Matplotlib
- Seaborn
- Pandas
JupyterLab app with STATA feature provides access to
- Stata (stata license to be provided by the user)
- nipype
- FreeSurfer
- FSL
- tensorflow
- torch
- cntk
- keras
- scikit-Learn
- MLlib