David YunTe Lin's Projects
Course material for BIO 260 and CSCI E-107 in Spring 2016
repository for data for Spring 2016
cfDNA Sequencing Pipeline with UMI
basic walk-throughs for alignment and variant calling from NGS sequencing data
A curated list of awesome Bioinformatics libraries and software.
Python package to calculate various sample contamination metrics.
SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
A simple implementation of the circular binary segmentation algorithm in python
Essential Cheat Sheets for deep learning and machine learning researchers https://medium.com/@kailashahirwar/essential-cheat-sheets-for-machine-learning-and-deep-learning-researchers-efb6a8ebd2e5
Modular bioinformatics pipelines for the CMO
CNV simulation scripts and meta data
Copy number variant detection from targeted DNA sequencing
Complete solutions for Stanford CS224n, winter, 2019
My solutions to the practical assignments of CS224n (Natural Language Processing with Deep Learning) [Stanford University-Winter 2019]
Repository for data in datasciencelabs
Official content for the Spring 2015 Boston University CS591 "Tools and Techniques for Data Mining and Applications" course
Disease phenotype association with deletion and their locations
The Variant Effect Predictor predicts the functional effects of genomic variants
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
Interpreting cancer genomics data
Library and tool for annotating MAF files using Genome Nexus Webserver API
Archive of the SOLiD preprocessing scripts by Ariella Sasson & Todd Michael originally hosted at http://hts.rutgers.edu/filter
Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol.
Microassembly based somatic variant caller for NGS data
Solutions and algorithms for Speech and Language Processing (3rd ed. draft)
JavaScript mutation needle plot
Lollipop-style mutation diagrams for annotating genetic variations.