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2024_interview

ai_handson

amplificationtimer

Code for timing amplifications

battenberg

Battenberg R package for subclonal copynumber estimation

capseg

CapSeg - Copy Number from Exome Sequencing

charger

Characterization of Germline variants

cottrazm

Construct Tumor Transition Zone Microenvironment

dpclust3p

Dirichlet Process Clustering Pre-Processing Pipeline

gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4

mutationtimer

An R package to time somatic mutations

nextflow-oje

phylogicndt_focal

sarek_dn

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

scevan

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

snubioinfo-test-git

tutorial

usb-modules-v2

yart

RMarkdown Template for writing PDF reports