Andrea-JG

Data-Science-Cheatsheet

A helpful 5-page machine learning cheatsheet to assist with exam reviews, interview prep, and anything in-between.

In-depth-NGS-Data-Analysis-Course

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

swarm_learning

Scripts for figures and calculations of the manuscript by Warnat-Herresthal el al. 2020

training-modules

A collection of modules that are combined into 1-5 day workshops on computational topics for the childhood cancer research community.

Intro-to-rnaseq-hpc-salmon

tnbc_scrnaseq

Drews2022_CIN_Compendium

Main repository for Drews et al. (Nature, 2022)

EaCoN

Easy Copy Number !

OpenPedCan-analysis

The analysis repository for the Open Pediatric Cancer Project

TILs_Analysis

Pan-cancer tils analysis study by Hongming Xu

PlotCNV

An R package to create a pretty Copy Number Variant plot from a segments file

compbio-galaxy-wrappers

OHSU Galaxy wrappers.

create-pptc-pdx-oncoprints

As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of these models is required to enable PPTC investigators to develop robust "responder hypotheses" when drug activity is observed. With funding provided by Alex's Lemonade Stand Foundation, we genomically characterize a major subset of 286 PDX models. We use whole exome sequencing, transcriptome sequencing, and SNPArray to characterize the tumor models. The focus on DNA and RNA sequencing data mirrors the current standard practice in most clinical diagnostics lab that use these technologies to detect the spectrum of targetable mutations, gene amplifications, and gene fusion events relevant to preclinical drug development.

cna-processing

Script for taking the output of the GISTIC2.0 module and converting the data for use with MAGI, HotNet2, and CoMEt.

staDRIP

Code and PCS documentation for staDRIP paper

crpc-sv-pattern-study

regNet

regNet is an R package that utilizes gene expression and copy number data to learn regulatory networks for the quantification of potential impacts of individual gene expression alterations on user-defined target genes via network propagation.

gistic_plot

miRDriver

A computational tool to infer copy number derived miRNA-gene networks in cancer.

CZI

CZI Project Results

cnRegionPlot

A R script to plot the segment-level copy number data

plotgistic

scripts to create nice gistic visualisations

copy-number-plotting

Plotting geneCN and ichorCNA together

hmmcopy_refs

Scripts to generate gc and map files for hmmcopy