This repo contains PRM analysis of Magnaporthe oryzae strains Guy11 vs dpmk1.
1499
Performed as described in the repo .Rmd
using the tools previously developed in pepdiff
https://github.com/TeamMacLean/pepdiff.
- 6-12-2021
Added
analysis/001_data_preparation.Rmd
,analysis/002_data_checks.Rmd
andanalysis/003_da_estimates.Rmd
; generating resultsanalysis/003_differential_abundance_<sample>_estimates.xslx
.
Finalised replacement scheme and performed final da estimates. Performed k-means clustering analysis
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26-10-22 [CJ] GO enrichment analysis for each of the five clusters.
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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.
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15-12-22 [CJ] Qualitative comparison PRM and MS1 (based on visual trends).
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27-01-2023 [CJ] MS1 heatmap for select pathways.
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20-03-2023 [CJ] Barplots for selected peptides from the MS1 dataset.
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Re-organise directories for input files and output files>> project now contains directories for data, results, and graphics.