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FireCloud implementation of FACETS
Dockerized and FireCloud implementation for MSI sensor
Precision Heuristics for Interpreting the Alteration Landscape
DeconstructSigs algorithm in python.
A simple filter to annotate and filter somatic variants based on their observed allele counts in ExAC
FireCloud method: high-throughput visualization of splice junctions using ggsashimi package
A multithreaded Python implementation of Beryl Cummings' MendelianRNA-seq algorithm
A script that adds columns with arm and band-level information to any tab-separated file. Intended primarily for use with .seg-format files, but applicable across formats.
Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
R2D2: RNA Normal/RNA Tumor, DNA Normal/DNA Tumor Analysis
Format mutations for oncoprint
This script takes in a tab-separated file containing at least one column of Ensembl IDs and a string indicating the header for this column, and outputs a tab-separated file identical to the input file except that it has an additional column containing mapped HGNC gene symbols for each row.
Combine snv maf, indel maf, and titan allelic copy number calls, from either FACETS or TITAN, into the .tsv input PyClone requires.
Contains TPM matrix (produced by RSEM) for pre-treatment samples from N = 42 ipilimumab-treated melanoma patients published in Van Allen et al. Science 2015.
Dockerfiles for Miniconda
Mouw et. al 2016, Genomic Evolution After Chemoradiotherapy in Anal Squamous Cell Carcinoma
A class for calculating maf set intersections, with example scripts demonstrating usage.
Coding exercises for budding computational biologists
Pipeline to call somatic cancer neoantigens from mutations in patient tumor DNA
Dockers for Matlab Compiler Runtime (MCR)
Given gene annotated segtab files from ABSOLUTE generate arm and band level annotations and calls for amplifications, LOH, and deletions based on process from Brastianos, Carter et al Cancer Discovery 2015
This workflow can be used to visualize the data from an *ABS_MAF.txt absolute file output. Both detection power and genomic locus are plotted for all SNPs, along with clustering information based on cancer cell fraction.
Algorithm for quantifying the number of translocation reads and wild-type reads in plasma samples with detectable ctDNA
Cohort analysis of TCGA mc3 with PHIAL
Computational analysis of clinically actionable genomic features: Precision Heuristics for Interpreting the Alteration Landscape (PHIAL) - AACR 2017