shihuang047

Shi Huang's repositories

2bRAD-M-manuscript

This repository provided all source data and codes for generation of all results in the 2bRAD-M manuscript.

Language:Jupyter Notebook000

This repository provided all source data and codes for generation of all results in the 2bRAD-M manuscript. The preprint version of this paper has been available at biorxiv: Species-resolved sequencing of low-biomass microbiomes by 2bRAD-M by Zheng Sun, Shi Huang, Pengfei Zhu, Lam Tzehau, Helen Zhao, Jia Lv, Rongchao Zhang, Lisha Zhou, Qianya Niu, Xiuping Wang, Meng Zhang, Gongchao Jing, Zhenmin Bao, Jiquan Liu, Shi Wang, Jian Xu. BioRxiv, doi: https://doi.org/10.1101/2020.12.01.405647

Language:Jupyter Notebook000

2bRAD_denovo

Genome-wide de novo genotyping with 2bRAD

Language:Perl000

alphafold

Open source code for AlphaFold.

Apache-2.0000

BacDiveR

R client for the DSMZ's Bacterial Diversity Metadatabase (former contact: @katrinleinweber)

Language:RMIT010

bisb-bootcamp-2020-module08

Language:PythonBSD-3-Clause010

CAMISIM

CAMISIM: Simulating metagenomes and microbial communities

Language:PythonApache-2.0010

curatedMetagenomicData

Curated and processed metagenomic data through ExperimentHub

NOASSERTION000

DistVis

Language:R000

docs

Source repository for https://docs.qiime2.org

Language:PythonBSD-3-Clause010

gemelli

tensor decomposition for spatiotemporal omics data

Language:Jupyter NotebookBSD-3-Clause010

ipyrad

Interactive assembly and analysis of RAD-seq data sets

GPL-3.0000

kraken2

The second version of the Kraken taxonomic sequence classification system

MIT000

LightGBM

A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM or MART) framework based on decision tree algorithms, used for ranking, classification and many other machine learning tasks.

Language:C++MIT010