Alvin Qin's repositories
ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
depmap_omics
What you need to process the Quarterly DepMap-Omics releases from Terra
pyrovelocity
Probabilistic model of RNA velocity
chirho
An experimental language for causal reasoning
comprehensive-rust
This is the Rust course used by the Android team at Google. It provides you the material to quickly teach Rust to everyone.
ctat-mutations
Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
dowhy
DoWhy is a Python library for causal inference that supports explicit modeling and testing of causal assumptions. DoWhy is based on a unified language for causal inference, combining causal graphical models and potential outcomes frameworks.
gcp-for-bioinformatics
GCP for Bioinformatics Researchers
gffcompare
classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
GMAP-fusion
source code for GMAP-fusion
hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
linux
Linux kernel source tree
llama2.c
Inference Llama 2 in one file of pure C
mapquik
Efficient low-divergence mapping of long reads in minimizer space
pangene
WIP: Constructing a pangenome gene graph
pertpy
Perturbation Analysis in the scverse ecosystem.
PhyloVelo
PhyloVelo, Phylogeny-based transcriptomic velocity of single cells
pml2-book
Probabilistic Machine Learning: Advanced Topics
Rust
All Algorithms implemented in Rust
scikit-llm
Seamlessly integrate LLMs into scikit-learn.
Sniffles
Structural variation caller using third generation sequencing
SUPPA
SUPPA: Fast quantification of splicing and differential splicing
vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms