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About me

  • šŸ‘‹ Hello, I am Mingkee and I am a researcher.

  • šŸ‘€ I am interested in computational biology, genomics and transcriptomics.

  • šŸ” I like finding biological answers in big data.

  • šŸŒ± Iā€™m currently learning machine-learning techniques to apply to genomics data.

  • šŸ˜„ Pronouns: she/her

Mingkee Achom's Projects

canopy icon canopy

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.

cworld-dekker icon cworld-dekker

perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)

deeplearningexamples icon deeplearningexamples

State-of-the-Art Deep Learning scripts organized by models - easy to train and deploy with reproducible accuracy and performance on enterprise-grade infrastructure.

gatk4-data-processing icon gatk4-data-processing

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

genomeinfodb icon genomeinfodb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

gistic2 icon gistic2

Genomic Identification of Significant Targets in Cancer (GISTIC), version 2

hatchet icon 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.

hic_tools icon hic_tools

A collection of tools for Hi-C data analysis

phylogicndt icon phylogicndt

Forked repository of the PhylogicNDT code with updates to get the dockerfile working

purecn icon purecn

Copy number calling and variant classification using targeted short read sequencing

pyenv icon pyenv

Simple Python version management

pytorch icon pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

snakemake-trcc icon snakemake-trcc

Personal repository to store syntax, examples and notes for Snakemake collected from different resources

titancna_10x_snakemake icon titancna_10x_snakemake

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.

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