Git Product home page Git Product logo

phylogenetic-dirichlet-multinomial-model-for-microbiome-data's Introduction

Phylogenetic-Dirichlet-multinomial-model-for-microbiome-data

These R codes are for the paper "Phylogenetic Dirichlet-multinomial model for microbiome data" by Yunfan Tang, Ma Li and Dan L. Nicolae.

The AG raw data (OTU table, metadata and phylogenetic tree) in May 16 2016 batch can be downloaded from

ftp://ftp.microbio.me/AmericanGut/ag-May-16-2016/03-otus/notrim/gg-13_8-97-percent/97_otus.tree ftp://ftp.microbio.me/AmericanGut/ag-May-16-2016/03-otus/notrim/gg-13_8-97-percent/otu_table.biom ftp://ftp.microbio.me/AmericanGut/ag-May-16-2016/04-meta/ag-cleaned.txt

Program descriptions:

TailBound.R: Implements the union bound algorithm (Section 4.2). Also contains script to compare union bound with Monte Carlo simulations (Section 4.3).

AmericanGut.R: Two-sample testing (Section 5.1).

LRT.R: Likelihood ratio test for DM vs PhyloDM (Section 5.2).

ROC.R: Produces ROC curve and power curve by simulation (Section 5.3).

Read_hdf5biom.R: A publically available script to read sparse biom files.

SingleNodeOptimize.R: Source file for LRT.R.

TwoSampleNode.R: Source file for AmericanGut.R, LRT.R and ROC.R.

phylogenetic-dirichlet-multinomial-model-for-microbiome-data's People

Contributors

yunfantang avatar

Watchers

avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.