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ancombc

Differential abundance (DA) analysis for microbial absolute abundance data

animalcules

R shiny app for interactive microbiome analysis

awesome-network-analysis

A curated list of awesome network analysis resources.

bacterial_gwas_tutorial

Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop

clinical-micro-meta-integration

This pipeline from https://bitbucket.org/hellekp/clinical-micro-meta-integration

co-occurrence

R scripts for performing co-occurrence analyses

docs

Documentation of the Snakemake-Workflows project

explore-python

:green_book: The Beauty of Python Programming.

fastspar

Rapid and scalable correlation estimation for compositional data

groupedstats

Grouped statistical analysis in a tidy way

krakentools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

metaanalysisp

关注统计方法，宏基因组下游分析的流程

metaphinder

metapi

A pipeline to construct a genome catalogue from metagenomics data.

microbiome

microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

microbiomeviz

Visualize microbiome data with black magic ggtree

mldm

mLDM: a new hierarchical Bayesian statistical model for sparse microbial association discovery

network_meta

combine the network analysis method & figure

pytorch-template

PyTorch deep learning projects made easy.

rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

snpbac

SNP and variant calling pipeline for bacteria

sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

spieceasi

Sparse InversE Covariance estimation for Ecological Association and Statistical Inference

stabl

utilities

A repository of bioinformatics utilities and scripts commonly used in the Steven J. Hallam Laboratory in the Microbiology & Immunology Department of the University of British Columbia (UBC), Vancouver, British Columbia, Canada.