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2017-cicese-metagenomics

alto

'alto' is an R package that aligns topics from different LDA models, computes metrics for quantifying the goodness of alignment, and provides visualization functions to explore the alignment and robustness of topics across environments or LDA hyper-parameters.

amplicon

Statistics and visualization for amplicon data

ancom-bc-code-archive

Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction"

awesome-machine-learning

A curated list of awesome Machine Learning frameworks, libraries and software.

benchmark_microbiome_transformations

Code to reproduce the analyses from the paper "Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases"

brc_mh_bioinformatics

Collection of pipelines, workflows and scripts for processing SNP and gene expression arrays and NGS data

causal_inference_python_code

Python code for part 2 of the book Causal Inference: What If, by Miguel Hernán and James Robins

cbw2021_module2_16s_analysis

cclasso

CCLasso: Correlation Inference for Compositional Data through Lasso

cheatsheets

Official Matplotlib cheat sheets

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

data-science-cheatsheet

deep-learning-projects

Collection of deep learning scripts in Python and R

deepmicro

Deep representation learning for disease prediction based on microbiome data

dicom-containers

singularity and Docker containers to easily get started with common dicom tools

dmp

Codes and sample data supporting the Dutch Microbiome Project. The preprint is currently available at https://www.biorxiv.org/content/10.1101/2020.11.27.401125v1 and full data can be requested from EGA (https://ega-archive.org/studies/EGAS00001005027) and Lifelines biobank (https://www.lifelines.nl/researcher)

dsbook

Repository for data science book

emp

Code repository of the Earth Microbiome Project.

feature-selection-for-machine-learning

Code repository for the online course Feature Selection for Machine Learning

frontiers_2017

Supplement for Frontiers article

g2s

Deep learning predictor of stool microbiome configuration from oral microbiome data

gformula

The gfoRmula package implements the parametric g-formula in R. The parametric g-formula (Robins, 1986) uses longitudinal data with time-varying treatments and confounders to estimate the risk or mean of an outcome under hypothetical treatment strategies specified by the user.

ggclusternet

Microbial ecological network visualization clustering

glmmadaptive

GLMMs with adaptive Gaussian quadrature

groningen-microbiome

Microbiome Projects from the Department of Genetics and Department of Gastroenterology and Hepatology , University Medical Centre Groningen

huang2019science

Scripts for Arabidopsis triterpene

hyperimpute

A framework for prototyping and benchmarking imputation methods

ibean

Data repo for the ibean project of the AIR lab.

infographic

Infographic