Pinned Repositories
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
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.
scg
Software for inference of clonal genotypes using targeted single cell (nucleus) sequencing.
tap_cn_calling
tea
Tapestri express analysis
haochenz96's Repositories
haochenz96/tap_cn_calling
haochenz96/CLAM
Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
haochenz96/CNT-ILP
Integer Linear Program for the Copy-Number Tree Problem
haochenz96/DAb-seq
DAb-seq: combined single-cell DNA genotyping and protein quantification.
haochenz96/dndscv
dN/dS methods to quantify selection in cancer and somatic evolution
haochenz96/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.
haochenz96/IGV-snapshot-automator
Script to automatically create and run IGV snapshot batchscripts
haochenz96/itctools
Tools for setting up ITC experiments in an automated fashion using the Tecan EVO and Auto-iTC 200.
haochenz96/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.
haochenz96/scg
Software for inference of clonal genotypes using targeted single cell (nucleus) sequencing.
haochenz96/tea
Tapestri express analysis
haochenz96/prePOLAR-hz-analysis
haochenz96/python-lsf
Improved interface for the LSF batch job scheduler
haochenz96/TapAnalysisSmk
haochenz96/Tapestri_main_manuscript_analysis
haochenz96/TapVarCallSmk
Customized Tapestri pipeline
haochenz96/tea-viz
haochenz96/tempo
CCS research pipeline to process WES and WGS TN pairs
haochenz96/treeomics
Decrypting somatic mutation patterns to reveal the evolution of cancer