chengyao-peng Goto Github PK

amplicon_sequencing_pipeline

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

cada

combat-seq

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

deepmicro

Deep representation learning for disease prediction based on microbiome data

dowhy

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 graphical models and potential outcomes frameworks.

feature-engineering-and-feature-selection

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

google_nmt_tutorial

TensorFlow Neural Machine Translation Tutorial

kraken2

The second version of the Kraken taxonomic sequence classification system

krakentools

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

link-prediction

Representation learning for link prediction within social networks

lskscripts

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.

maml1.0

Automated machine learning model building pipeline for microbiome data

masterthesis

meta-signer

metaml

micnettoolbox

Deconstructing a microbial interaction network

microbiome

Microbiome repository

mirkatmc

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

nested-cross-validation

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.

pycombat

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.

qiime

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

rosalind-solutions

my solutions to problems from Rosalind.

struo2

Scalable creating/updating of metagenome profiling databases

sva-devel

triplot

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