Network construction, analysis, and comparison for microbial compositional data

A PyTorch Library for Meta-learning Research

A repository with scripts to infer and analyze microbial association networks for the MicW2Graph project

Scalable creating/updating of metagenome profiling databases

DoWhy is a Python library for causal inference that supports explicit modeling and testing of causal assumptions. DoWhy is based on a unified language for causal inference, combining causal graphic…

pyComBat is a Python 3 implementation of ComBat, one of the most widely used tool for correcting technical biases, called batch effects, in microarray expression data.

A Guide for Feature Engineering and Feature Selection, with implementations and examples in Python.

The Microbiome Regression-based Kernel Association Test for multi-categorical (nominal or ordinal) data

Deconstructing a microbial interaction network

Microbiome repository

The second version of the Kraken taxonomic sequence classification system

A placeholder for all my random scripts. Some scripts might eventually graduate and go to their own projects, so don't be surprised if anything leaves in the future.

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

Triplot: Instance- and data-level explanations for the groups of correlated features.

my solutions to problems from Rosalind.

Automated machine learning model building pipeline for microbiome data

Batch effect adjustment based on negative binomial regression for RNA sequencing count data

Deep representation learning for disease prediction based on microbiome data

Nested cross-validation for unbiased predictions. Can be used with Scikit-Learn, XGBoost, Keras and LightGBM, or any other estimator that implements the scikit-learn interface.

Pipeline for computing OTU tables from 16S or ITS amplicon sequencing data.

Representation learning for link prediction within social networks

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

TensorFlow Neural Machine Translation Tutorial