PySNAIL

Smooth-quantile Normalization Adaptation for Inference of co-expression Links (SNAIL) is a method that corrects for false-positive associations, which may form between lowly expressed genes after smooth quantile normalization of the data, and which may affect downstream co-expression network analysis. The PySNAIL software is developed by the Kuijjer’s Lab.

Table of Contents

• Installation
  • Environment Setting
  • Install Package
  • Example Dataset
• Quick Start
  • Reproduce Analysis in the Manuscript
• Manual
  • Correct Expression
  • Information of Input Data
  • Statistics of Qsmooth
  • Diagnosis of Qsmooth
• Documentation
  • pysnail.dataset
  • pysnail.qsmooth
  • pysnail.utils

• Index

Introduction

SNAIL is an alternative implementation of smooth quantile normalization (qsmooth), designed to correct false-positive gene associations in qsmooth-normalized RNA-Seq data. Specifically, instead of using the mean value of counts to normalize the expression of genes with the same read count, as is done in the original qsmooth algorithm, SNAIL uses median aggregation (step 7 and step 8 in the following figure). We developed PySNAIL as a standalone Python package supporting multi-thread optimization. We’ve also implemented a diagnostic function that computes the proportion of affected genes for each sample, to help detect whether smooth quantile normalization would introduce false-positive co-expression between genes in a specific dataset.

Issues

Please report any issue, feedback or bug report to the GitHub issues page.