Gang Yao's repositories
adotto
Working space for the GIAB TR benchmarking project
awesome-machine-learning
A curated list of awesome Machine Learning frameworks, libraries and software.
bento-tools
A Python toolkit for subcellular analysis of spatial transcriptomics data
build-your-own-x
Master programming by recreating your favorite technologies from scratch.
ChimeraTE
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
chroma
A generative model for programmable protein design
ColabFold
Making Protein folding accessible to all!
deepgoplus
DeepGO with GOPlus axioms
GenEra
genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families.
GENESPACE
An R package for synteny- and orthology-constrained comparative genomics
genomics-research
Google Genomics Research
GFF3toolkit
Python programs for processing GFF3 files
HLA-LA
Fast HLA type inference from whole-genome data
LLM-CookBook
面向开发者的 LLM 入门教程，吴恩达大模型系列课程中文版
LLM-Universe
大模型应用开发入门教程，在线阅读地址：https://datawhalechina.github.io/llm-universe/
pantera
Identification of transposable element families from pangenome polymorphisms
Plant-LncRNA-pipline
A computational pipeline providing significant improvement in plant lncRNA identification
polyBreedR
Using genome-wide markers for polyploid breeding
Populus_superpangenome
Scripts for suer-pangenome of Populus
pytorch-lightning
Pretrain, finetune and deploy AI models on multiple GPUs, TPUs with zero code changes.
RepeatOBserverV1
An R package to visualize chromosome scale repeat patterns and predict centromere locations.
resistify
To classifies plant NLRs by their protein domain and motif architecture
scarches
Reference mapping for single-cell genomics
Segment-Everything-Everywhere-All-At-Once
[NeurIPS 2023] Official implementation of the paper "Segment Everything Everywhere All at Once"
singularity
SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.
snpR
population genomics basic stats
SyntenyFinder
SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-level genome assemblies from NCBI.
TRTools
Toolkit for genome-wide analysis of tandem repeats
truvari
Structural variant toolkit for VCFs
wfmash
base-accurate DNA sequence alignments using WFA and mashmap2