Mingkee Achom's Projects
Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.
A set of hands-on tutorials for CUDA programming
perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
State-of-the-Art Deep Learning scripts organized by models - easy to train and deploy with reproducible accuracy and performance on enterprise-grade infrastructure.
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Genomic Identification of Significant Targets in Cancer (GISTIC), version 2
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.
HiC uniform processing pipeline
A collection of tools for Hi-C data analysis
Forked repository of the PhylogicNDT code with updates to get the dockerfile working
Copy number calling and variant classification using targeted short read sequencing
Simple Python version management
Tensors and Dynamic neural networks in Python with strong GPU acceleration
Personal repository to store syntax, examples and notes for Snakemake collected from different resources
Structural variation analysis of 10X Genomics linked-read data
Snakemake workflow for 10X Genomics WGS analysis using TitanCNA - GavinHaLab Forked Repo. Fixed the Issue I was getting from the original repo: Error: RangedData objects are deprecated and the coercion method from data.frame or DataTable to RangedData is now defunct. Please migrate your code to use GRanges or GRangesList objects instead.