Shi Huang (shihuang047)

shihuang047

Geek Repo

Company:UC San Diego

Location:La Jolla

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Shi Huang's repositories

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2bRAD-M-manuscript

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

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2bRAD-M-paper

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

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2bRAD_denovo

Genome-wide de novo genotyping with 2bRAD

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alphafold

Open source code for AlphaFold.

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BacDiveR

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

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CAMISIM

CAMISIM: Simulating metagenomes and microbial communities

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curatedMetagenomicData

Curated and processed metagenomic data through ExperimentHub

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docs

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

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gemelli

tensor decomposition for spatiotemporal omics data

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ipyrad

Interactive assembly and analysis of RAD-seq data sets

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kraken2

The second version of the Kraken taxonomic sequence classification system

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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.

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mlrMBO

Toolbox for Bayesian Optimization and Model-Based Optimization in R

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PM_Rscript

The Rscripts for microbiota analysis

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q2-breakaway

QIIME2 plug-in for breakaway

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qurro-mackerel-analysis

Simple re-analysis of mackerel and seawater marker gene sequencing samples in QIIME 2 + Songbird + Qurro

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SHOGUN

SHallow shOtGUN profiler

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stability-analyses

code for simulation studies and experimental microbiome data applications in Stability manuscript

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TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

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