codetrainee / Neutrophil-systems-biology

Source code and raw data for neutrophil systems biology paper

The repository hosts the source for neutrophil proteomics paper

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├── 2019-01-25-neutrophil-proteomics-data-analysis-following-influenza-or-bacterial-infection.html
├── 2019-01-25-neutrophil-proteomics-data-analysis-following-influenza-or-bacterial-infection.rmd
├── README.md
└── data
    ├── Neutrophil-proteomics-data-analysis-following-influenza-or-bacterial-infection
    │   ├── 20170428-Proteomics-201611-Requant.txt
    │   ├── 20170428-Proteomics-201612-Requant.txt
    │   ├── 20180206-Proteomics-201801-Requant.txt
    │   ├── 20181018-reactome-pathway-analysis.xlsx
    │   └── all-stat-gene-DAVID-database-GO-cell-compartment.txt
    ├── Rscripts
    │   ├── load_libraries.R
    │   └── utilities.R
    └── pkg_list.txt

Publication

https://doi.org/10.4049/jimmunol.1900337

Caution

The kmeans clustering results can't be reproduced in R 3.6 as they changed the behavior of set.seed. PR#17494

ComplexHeatmap 2.0 bundled in Biocondcutor 3.9 can't reproduce the results (mainly on appearance of the order of hierarchy clusters but doesn’t affect data interpretation).

To reproduce all results, R version should be under 3.6 and Biocondctor should be 3.8. The package information is included in the pkg_list.txt file under data