For running private Parabricks workflows on Amazon Omics

analysis pipeline for CODEC data

Structural variant and indel caller for mapped sequencing data

microsatellite instability detection using tumor only or paired tumor-normal data

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

Molecular International Prognostic Scoring System IPSS-M for Myelodysplastic Syndromes

Load, review and adjust facets fits

Voyager Backend

Computing with Python functions.

Toil API

Python package to calculate various sample contamination metrics.

Tools for copy-number analysis using FACETS

Concordance and contamination estimator for tumor-normal pairs

Python package and routines for merging SV VCF files

R datasets of GC percentages for human and mouse genomes

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

Script to automatically create and run IGV snapshot batchscripts

SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability…

Copy number calling and variant classification using targeted short read sequencing

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

toil wrapper for CNACS

👑 🐝 📊 Beyoncé colour palettes for R

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

Develop a knowledge-based approach using MSK-IMPACT data to build an automatic variant classifier