The following python modules are needed to reproduce the analysis
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numpy 1.22.4
pandas 1.5.3
session_info 1.0.0
structuremap 0.0.8
tqdm 4.65.0
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Python 3.9.12 (main, Apr 5 2022, 01:53:17) [Clang 12.0.0 ]
macOS-10.16-x86_64-i386-64bit
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The following R packages are needed to reproduce the analysis
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[1] ggforce_0.3.4 openxlsx_4.2.5 cowplot_1.1.1 pbapply_1.7-0
[5] ggpubr_0.4.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.9
[9] purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.8
[13] ggplot2_3.3.6 tidyverse_1.3.2 seqinr_4.2-16 here_1.0.1
[17] org.Hs.eg.db_3.15.0 org.Mm.eg.db_3.15.0 AnnotationDbi_1.58.0 IRanges_2.30.0
[21] S4Vectors_0.34.0 Biobase_2.56.0 BiocGenerics_0.42.0
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R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.4
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The jupyter notebooks 1_download_topological_domains.ipynb, 2_retrieve_annotated_alphafold.ipynb and 3_preprocess_sift_scores.ipynb are used to generate the needed inputs for the main.Rmd notebook, which uses all the structural, domain and conservation information to explore the properties of glycosites with different levels of microheterogeneity. The main.Rmd uses the preprocessed PTM tables provided in the manuscript as Supplementary Files.
To execute 3_preprocess_sift_scores.ipynb, precomputed SIFT scores for a given organism need to be retrieved from https://sift.bii.a-star.edu.sg/sift4g/ and collapsed to a single file. For 1_download_topological_domains.ipynb and 2_retrieve_annotated_alphafold.ipynb the only requirement is a stable internet connection.