gogleva / Marchantia

Reproducible scripts for Marchantia ms

Marchantia

Scripts for Marchantia II paper, mainly transcriptomics

Scripts:

DEG_analysis_Mpolymorpha_Ppalmivora.R

• Analysis of differentially expressed genes in M.polymorpha-P.palmivora (ARI-tdTomato) timecourse (1,2,3 and 4 dpi with correspondent mock samples).

• Volcano plots for pair-wise comparisons;

• Upset plots for up- and down-regulated genes;

• Heatmap, showing overall expression patterns of DEGs, identified in all pair-wise comparisons.

  This script requires 2 input data files:

  • data/FeartureCounts_STAR_Mpolymorpha.tsv - raw counts
  • data/sample_table_Mpolymorpha.csv - description of samples and conditions in M.polymorpha-P.palmivora (ARI-tdTomato) timecourse

DEG_analysis_Nbenthamiana_Ppalmivora.R

• Analysis of differentially expressed genes in N.benthamiana-P.palmivora (ARI-tdTomato) timecourse (14,24,48 and 72 hpi with correspondent mock samples).

• Volcano plots for pair-wise comparisons;

• Upset plots for up- and down-regulated genes;

• Heatmap, showing overall expression patterns of DEGs, identified in all pair-wise comparisons.

  This script requires 2 input data files:

  • data/FeartureCounts_STAR_Nbenthamiana.csv - raw counts
  • data/sample_table_Nbenthamiana.csv - description of samples and conditions in M.benthamiana-P.palmivora (ARI-tdTomato) timecourse

ortholog_expression_analysis_Mpolymorpha_Nbenthamiana.R

• DEG analysis, filter genes by adjusted p-value, keep all LFC

• parse OrthoDinfer outputs

• visualise expression patterns of single-copy orthologs during comparable stages of infection

  This script requires the following input files:

  • data/FeartureCounts_STAR_Mpolymorpha.tsv - raw counts
  • data/sample_table_Mpolymorpha.csv - description of samples and conditions in M.polymorpha-P.palmivora (ARI-tdTomato) timecourse
  • data/FeartureCounts_STAR_Nbenthamiana.csv - raw counts
  • data/sample_table_Nbenthamiana.csv - description of samples and conditions in M.benthamiana-P.palmivora (ARI-tdTomato) timecourse
  • Orthogroups.csv - raw output from OrthoFinder, orthogroups between M.polymorpha and N.benthamiana
  • SingleCopyOrthogroups.txt - list of orthogroups with single-copy genes in M.polymorpha and N.benthamiana
  • Mpolymorpha_tidy_annotation.csv - summary tidy functional annotation for M.polymorpha