index.Rmd

--- 
title: "Introduction to SIPmg"
author: "Pranav Sampara, Kate Waring, Ryan Ziels"
date: "`r Sys.Date()`"
documentclass: book
cover-image: "images/EMBERR_logo-2.png"
description: |
  SIPmg is a statistical analysis package as part of a stable isotope probing
  (SIP) metagenomics study to identify isotope incorporating MAGs.The package
  utilizes either the qSIP model, ΔBD method, or DeSeq2-based methods such as
  HR-SIP and MW-HR-SIP based on the HTSSIP package. For more information on HTSSIP
  R package, please visit their vignette
output:
  bookdown::html_document
site: bookdown::bookdown_site
github-repo: ZielsLab/SIPmg.github.io
---

# Introduction

The SIPmg R package was designed to enable the exploration and statistical analysis of qSIP metagenomics data. Particularly, this package allows the identification of isotope incorporators and quantifies isotopic enrichment.

Please check out introductory vignettes with some [background information](#background) and a [quick example pipeline](#quick-example), before checking out vignettes on:

[Coverage normalization and scaling based on linear regression model](#scaling-coverage-data)

[Identification of incorporators based on qSIP, ΔBD, or DESeq2 methods](#identifying-incorporators)