HLA-I PTM Analysis

Analysis of post-translational modifications on HLA class I presented peptides from the JY cell line.

Caron Laboratory, Yale University

Data

Cell line: JY (HLA-A02:01, B07:02, C*07:02)
Peptide length: 8-14 amino acids
PTMs: Phosphorylation, Cysteinylation, Deamidation, Acetylation, Methylation, Dimethylation, Citrullination, Oxidation, Ubiquitination, N-Glycosylation, SUMOylation

Rscript run_all_figures.R

Figures and data tables are saved to figure_panels/

Report: HLA-I_PTM_Analysis_Report.pdf

Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
figure_panels		figure_panels
.gitignore		.gitignore
Figure1_Composition.R		Figure1_Composition.R
Figure2_LengthDistribution.R		Figure2_LengthDistribution.R
Figure4A_Circos.R		Figure4A_Circos.R
Figure4B2_Position_Heatmap_ByPTM.R		Figure4B2_Position_Heatmap_ByPTM.R
Figure4B_Position_Heatmap.R		Figure4B_Position_Heatmap.R
Figure4C_PositionDensity.R		Figure4C_PositionDensity.R
Figure4X_Position_P1P14.R		Figure4X_Position_P1P14.R
Figure5A_StrongBinders.R		Figure5A_StrongBinders.R
Figure5B_ELRank_Distribution.R		Figure5B_ELRank_Distribution.R
Figure6DE_Improved.R		Figure6DE_Improved.R
Figure6_SpecificPTMs.R		Figure6_SpecificPTMs.R
HLA-I_PTM_Analysis_Report.md		HLA-I_PTM_Analysis_Report.md
HLA-I_PTM_Analysis_Report.pdf		HLA-I_PTM_Analysis_Report.pdf
README.md		README.md
data_loader.R		data_loader.R
md_to_pdf.py		md_to_pdf.py
render_report.R		render_report.R
run_all_figures.R		run_all_figures.R