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verta_jones_elife_2019's Introduction

README

This repository contains scripts used in the analysis of

  • Verta J-P & Jones FC: Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks, eLife 2019

Communications should be sent to

Steps to produce primary alignments and perform CuffLinks expression analyses described in methods section of the article.

Analysis steps (in order of results in article)

  • PCAanalysis.r
  • PCAloadingPlot.r
  • DEanalysisPureEcotypes.r
  • PCAvsDE.r
  • makePopGenTracksTSS.r
  • popGenPlotsTSS.r
  • CSSversusCompPC.r
  • combineAseReadCountFiles.r
  • normalizeInfCounts.r
  • individualASE.r
  • CisVsTrans.r
  • xlocVsEffect.r
  • parseEffectsPerCross.r
  • CisTransFreqs.r
  • CisTransOverrepresentation.r
  • salinityVsPCA.r
  • epistasis.r

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