Whole genome sequence simulation of DUF1220 domains and testing of alignment strategies

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing

R Package to compare copy number variant (CNV) results from multiple samples or methods

R package for estimating copy-number variation from targeted DNA sequencing

Processing DNA Copy Number (CN) Data for Detection of CN Events

MSKCC CMO Innovation Lab

Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)

Annotation structure variant

Containerized workflow for single cell detection of loss of Y chromosome and other mosaic chromosomal alterations in chronic kidney disease

CNprep — Pre-process DNA Copy Number (CN) Data for Detection of CN Events

WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication

Contains the code and scripts used to process and analyze the data for my analysis of super-enhancer function in ovarian cancer cells (OVCAR3) and in patient RNA-seq and Copy Number data from The Cancer Genome Atlas (TCGA). This project was published by Nat. Communications in July 2022. https://doi.org/10.1038/s41467-022-31919-8

Inference of copy number and mutation multiplicity in oncology

Epicopy R package for CNV identification from methylation microarrays.

Deep multiple instance learning model for predicting deletion pathogenicity and gene haploinsufficiency.

@mapk14#

Framework to benchmark germline copy-number variant detection tools from NGS data