/PD_PRO_1499_06122021_PRM2

This repo contains PRM analysis of _Magnaporthe oryzae_ strains _Guy11_ vs _dpmk1_.

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PRM analysis M.oryzae Guy11 vs dpmk1

This repo contains PRM analysis of Magnaporthe oryzae strains Guy11 vs dpmk1.

SL TICKETS

1499

Info

Performed as described in the repo .Rmd using the tools previously developed in pepdiff https://github.com/TeamMacLean/pepdiff.

Lab Book

  • 6-12-2021 Added analysis/001_data_preparation.Rmd, analysis/002_data_checks.Rmd and analysis/003_da_estimates.Rmd; generating results analysis/003_differential_abundance_<sample>_estimates.xslx.

Finalised replacement scheme and performed final da estimates. Performed k-means clustering analysis

  • 26-10-22 [CJ] GO enrichment analysis for each of the five clusters.

  • 01-12-22 [CJ] Add one heatmap showing selected targets (direct targets of pmk1) as annotation and one heatmap only displaying the selected targets; also add GO enrichement of the proteins corresponding to the selected targets.

  • 15-12-22 [CJ] Qualitative comparison PRM and MS1 (based on visual trends).

  • 27-01-2023 [CJ] MS1 heatmap for select pathways.

  • 20-03-2023 [CJ] Barplots for selected peptides from the MS1 dataset.

TODO

  • Re-organise directories for input files and output files >> project now contains directories for data, results, and graphics.