/Marchantia

Reproducible scripts for Marchantia ms

Primary LanguageR

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