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2brad-m

2brad-m-manuscript

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

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

2brad_denovo

Genome-wide de novo genotyping with 2bRAD

adversarial-robustness-toolbox

Python library for adversarial attacks and defenses (evasion, poisoning) for neural networks with multiple framework support

age-prediction

aihn-ucsd

This repo is used to release code that is generated by the AI Horizons Network as needed to supplement conference papers and workshops.

alphafold

Open source code for AlphaFold.

american-gut-analyses

assertthat

User friendly assertions for R

auto-sklearn

Automated Machine Learning with scikit-learn

bacdiver

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

biom-format

The Biological Observation Matrix (BIOM) Format Project

bisb-bootcamp-2020-module08

calour

exploratory and interactive microbiome analyses based on heatmaps

camisim

CAMISIM: Simulating metagenomes and microbial communities

crossranger

curatedmetagenomicdata

Curated and processed metagenomic data through ExperimentHub

deicode

Robust Aitchison RPCA on sparse omics datasets

distvis

dmbc

A Bayes classifier based on the Dirichlet-Multinomial distribution

doc

Dissimilarity Overlap Curve analysis

docs

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

feast

Fast expectation maximization for microbial source tracking

gemelli

tensor decomposition for spatiotemporal omics data

harrietr

An `R` package for various phylogenetic and evolutionary biology data manipulations

hierarchicalfeatureengineering

Hierarchical Feature Engineering for Microbiota (16S rRNA profiles), as provided by OTU tables of relative abundances.

imp_analyses

immigrant microbiome project related analyses

ipyrad

Interactive assembly and analysis of RAD-seq data sets

kraken2

The second version of the Kraken taxonomic sequence classification system