Data Analysis of SARS-CoV2/SARS-CoV project

A collection of R and Julia scripts for the analysis of data for "SARS-CoV-2/SARS-CoV" project.

DOI

Name		Name	Last commit message	Last commit date
Latest commit History 321 Commits
.gitignore		.gitignore
Manifest.toml		Manifest.toml
Project.toml		Project.toml
README.md		README.md
analyze_apms.R		analyze_apms.R
analyze_cov2el_proteome.R		analyze_cov2el_proteome.R
analyze_cov2ts_phospho.R		analyze_cov2ts_phospho.R
analyze_cov2ts_proteome.R		analyze_cov2ts_proteome.R
analyze_oeproteome.R		analyze_oeproteome.R
analyze_parsars_fp.R		analyze_parsars_fp.R
analyze_parsars_ptm.R		analyze_parsars_ptm.R
apms_enrichment_analysis.jl		apms_enrichment_analysis.jl
apms_network_layout.jl		apms_network_layout.jl
archpc.julia.env		archpc.julia.env
assemble_fits_apms.R		assemble_fits_apms.R
assemble_fits_cov2el_proteome.R		assemble_fits_cov2el_proteome.R
assemble_fits_cov2ts_phospho.R		assemble_fits_cov2ts_phospho.R
assemble_fits_cov2ts_proteome.R		assemble_fits_cov2ts_proteome.R
assemble_fits_oeproteome.R		assemble_fits_oeproteome.R
assemble_fits_parsars_fp.R		assemble_fits_parsars_fp.R
assemble_fits_parsars_ptm.R		assemble_fits_parsars_ptm.R
cov2.Rproj		cov2.Rproj
cov2_plots_common.R		cov2_plots_common.R
cov2ts_phospho_enrichment_analysis.jl		cov2ts_phospho_enrichment_analysis.jl
cov2ts_phospho_prepare.jl		cov2ts_phospho_prepare.jl
cov2ts_proteome_enrichment_analysis.jl		cov2ts_proteome_enrichment_analysis.jl
expl2_dia_calib.jl		expl2_dia_calib.jl
generate_apms_graphml.R		generate_apms_graphml.R
generate_cellline_fasta.jl		generate_cellline_fasta.jl
generate_cov_fasta.R		generate_cov_fasta.R
global_infection_stats.R		global_infection_stats.R
hhotnet_perm_treecut_stats_chunk.cm2_lrz.sh		hhotnet_perm_treecut_stats_chunk.cm2_lrz.sh
hhotnet_perm_treecut_stats_chunk.jl		hhotnet_perm_treecut_stats_chunk.jl
hhotnet_perm_treecut_stats_chunk.sge.sh		hhotnet_perm_treecut_stats_chunk.sge.sh
hhotnet_perm_trees_chunk.cm2_lrz.sh		hhotnet_perm_trees_chunk.cm2_lrz.sh
hhotnet_perm_trees_chunk.sge.sh		hhotnet_perm_trees_chunk.sge.sh
hotnet_analysis.jl		hotnet_analysis.jl
hotnet_cm2lrz.julia.env		hotnet_cm2lrz.julia.env
hotnet_perm_chunk.cm2_lrz.sh		hotnet_perm_chunk.cm2_lrz.sh
hotnet_perm_chunk.jl		hotnet_perm_chunk.jl
hotnet_perm_chunk.sge.sh		hotnet_perm_chunk.sge.sh
hotnet_perm_chunk_assemble.jl		hotnet_perm_chunk_assemble.jl
hotnet_sge.julia.env		hotnet_sge.julia.env
hotnet_treestats_chunk.cm2_lrz.sh		hotnet_treestats_chunk.cm2_lrz.sh
hotnet_treestats_chunk.jl		hotnet_treestats_chunk.jl
hotnet_treestats_chunk.sge.sh		hotnet_treestats_chunk.sge.sh
infection_enrichment_analysis.jl		infection_enrichment_analysis.jl
match_protgroups.jl		match_protgroups.jl
msglm_fit_chunk_apms.R		msglm_fit_chunk_apms.R
msglm_fit_chunk_apms.lrz_cm2.sh		msglm_fit_chunk_apms.lrz_cm2.sh
msglm_fit_chunk_apms.serial_muc.sh		msglm_fit_chunk_apms.serial_muc.sh
msglm_fit_chunk_apms.sge.sh		msglm_fit_chunk_apms.sge.sh
msglm_fit_chunk_cov2el_proteome.R		msglm_fit_chunk_cov2el_proteome.R
msglm_fit_chunk_cov2el_proteome.lrz_cm2.sh		msglm_fit_chunk_cov2el_proteome.lrz_cm2.sh
msglm_fit_chunk_cov2ts_phospho.R		msglm_fit_chunk_cov2ts_phospho.R
msglm_fit_chunk_cov2ts_phospho.lrz_cm2.sh		msglm_fit_chunk_cov2ts_phospho.lrz_cm2.sh
msglm_fit_chunk_cov2ts_proteome.R		msglm_fit_chunk_cov2ts_proteome.R
msglm_fit_chunk_cov2ts_proteome.lrz_cm2.sh		msglm_fit_chunk_cov2ts_proteome.lrz_cm2.sh
msglm_fit_chunk_oeproteome.R		msglm_fit_chunk_oeproteome.R
msglm_fit_chunk_oeproteome.lrz_cm2.sh		msglm_fit_chunk_oeproteome.lrz_cm2.sh
msglm_fit_chunk_parsars_fp.R		msglm_fit_chunk_parsars_fp.R
msglm_fit_chunk_parsars_fp.lrz_cm2.sh		msglm_fit_chunk_parsars_fp.lrz_cm2.sh
msglm_fit_chunk_parsars_mqphospho.R		msglm_fit_chunk_parsars_mqphospho.R
msglm_fit_chunk_parsars_ptm.R		msglm_fit_chunk_parsars_ptm.R
msglm_fit_chunk_parsars_ptm.lrz_cm2.sh		msglm_fit_chunk_parsars_ptm.lrz_cm2.sh
oeproteome_enrichment_analysis.jl		oeproteome_enrichment_analysis.jl
parsars_fp_timeseries.R		parsars_fp_timeseries.R
parsars_mqphospho_prepare.jl		parsars_mqphospho_prepare.jl
parsars_phospho_enrichment_analysis.jl		parsars_phospho_enrichment_analysis.jl
parsars_phospho_prepare.jl		parsars_phospho_prepare.jl
parsars_ptm_prepare.jl		parsars_ptm_prepare.jl
parsars_ptm_timeseries.R		parsars_ptm_timeseries.R
plot_misc_heatmaps.jl		plot_misc_heatmaps.jl
prepare_data_apms.R		prepare_data_apms.R
prepare_data_common.R		prepare_data_common.R
prepare_data_cov2el_proteome.R		prepare_data_cov2el_proteome.R
prepare_data_cov2ts_phospho.R		prepare_data_cov2ts_phospho.R
prepare_data_cov2ts_proteome.R		prepare_data_cov2ts_proteome.R
prepare_data_oeproteome.R		prepare_data_oeproteome.R
prepare_data_parsars_fp.R		prepare_data_parsars_fp.R
prepare_data_parsars_mqphospho.R		prepare_data_parsars_mqphospho.R
prepare_data_parsars_phospho.R		prepare_data_parsars_phospho.R
prepare_data_parsars_ptm.R		prepare_data_parsars_ptm.R
prepare_data_parsars_rnaseq.R		prepare_data_parsars_rnaseq.R
prepare_suppl_reports.R		prepare_suppl_reports.R
protregroup_apms.jl		protregroup_apms.jl
protregroup_cov2el_proteome.jl		protregroup_cov2el_proteome.jl
protregroup_oeproteome.jl		protregroup_oeproteome.jl
protregroup_parsars_fp.jl		protregroup_parsars_fp.jl
ptm_scales_normalize.stan		ptm_scales_normalize.stan
qep5_apms_calib.jl		qep5_apms_calib.jl
qx7_dia_phospho_calib.jl		qx7_dia_phospho_calib.jl
qx7_dia_proteome_calib.jl		qx7_dia_proteome_calib.jl
qx8_dia_calib.jl		qx8_dia_calib.jl
setup_modelobj.R		setup_modelobj.R
viral_ptms_plots.R		viral_ptms_plots.R

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