Flakaliden 2011 analysis

Source code for the Metatranscriptomics captures the destabilised mycorrhizal economy in nutrient enriched boreal forests
Manuscript homepage

doc

Folder containing metadata and the ENA xml submission files

Spruce 2011

Folder spruce-roots-2011/pipeline

• pre-processing scripts

Folder spruce-roots-2011/src/R

• differentialExpression.Rmd

  • Biological QA
  • Differential expression analysis
  • Data preparation for Seidr

• networkClustering.Rmd

  • Networks clustering
  • Cluster enrichment

• TAtool_data

  • Scripts to format the data for the visualization app

Spruce 2012

Folder spruce-roots-2012/src/R

• differentialExpression.Rmd

  • Biological QA
  • Differential expression analysis

• differentialExpression_5year_included.Rmd

  • Biological QA
  • Differential expression analysis
  • Includes 5 year fertilisation for future analysis

Fungi 2011

• TAtool_data

  • Scripts to format the data for the visualization app

• differentialExpression_ko.Rmd

  • Biological QA
  • Differential expression analysis
  • Data preparation for Seidr

• differentialExpression_transcripts.Rmd

  • Biological QA
  • Differential expression analysis

• differentialExpression_fungi_species.Rmd

  • Biological QA
  • Differential expression analysis
  • Data preparation for Seidr

• megaData.R

  • Creates a data frame with all the fungi information

• networkThreshold_fungi_ko.Rmd

  • KO hard threshold analysis

• networkClustering_fungi.Rmd

  • Networks clustering
  • Cluster enrichment

• prepareSpeciesNetwork.Rmd

  • Data preparation for Seidr

Fungi 2012

Folder fungi-2012/src/R

• differentialExpression_ko.Rmd
  • Biological QA
  • Differential expression analysis
• megaData.R
  • Creates a data frame with all the fungi information

Common

Folder src/R

• correlationClusterAnalysis_*.Rmd

  • Correlation analysis based on module similarity

• bulkCorrelationAnalysis_*.Rmd

  • Correlation analysis results grouped and analysed

• differentialExpression_*.Rmd

  • differential expression comparative between 2011 and 2012 datasets

• splitEnr*_Rmd

  • Split network modules analysis and enrichment