haochenz96 Goto Github PK

clam

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

cnt-ilp

Integer Linear Program for the Copy-Number Tree Problem

dab-seq

DAb-seq: combined single-cell DNA genotyping and protein quantification.

dndscv

dN/dS methods to quantify selection in cancer and somatic evolution

hatchet

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

igv-snapshot-automator

Script to automatically create and run IGV snapshot batchscripts

itctools

Tools for setting up ITC experiments in an automated fashion using the Tecan EVO and Auto-iTC 200.

mosaic

Mosaic (custom) is adapted from Mission Bio's mosaic package which is used to analyze single-cell DNA sequencing data generated by the Tapestri machine.

prepolar-hz-analysis

python-lsf

Improved interface for the LSF batch job scheduler

scg

Software for inference of clonal genotypes using targeted single cell (nucleus) sequencing.

tapestri_main_manuscript_analysis

tea

Tapestri express analysis

tea-viz

tempo

CCS research pipeline to process WES and WGS TN pairs

treeomics

Decrypting somatic mutation patterns to reveal the evolution of cancer