├── .DS_Store ├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── Meta └── vignette.rds ├── NAMESPACE ├── NEWS ├── PhosMap.Rproj ├── R ├── analysis_deps_anova.R ├── analysis_deps_limma.R ├── analysis_deps_sam.R ├── check_mea_input.R ├── compute_kses.R ├── construct_pwm.R ├── extract_psites_score.R ├── fore_seq_to_motif.R ├── formatted_output_mef_results.R ├── generate_psites_score_file.R ├── get_aligned_seq_for_mea.R ├── get_colors_for_discrete_value.R ├── get_combined_data_frame.R ├── get_df_with_AAs_i.R ├── get_file_info_from_dir.R ├── get_file_suffix.R ├── get_filtered_df.R ├── get_foreground_df_to_motifs.R ├── get_foreground_seq_to_motifs.R ├── get_global_background_df.R ├── get_ka_by_mean_or_mlr.R ├── get_ksea_regulons_info.R ├── get_ksea_result_list.R ├── get_kses.R ├── get_list_with_filtered_sites.R ├── get_merged_phospho_df.R ├── get_modification_index.R ├── get_motif_analysis_summary.R ├── get_motifs_list.R ├── get_normalized_data_FOT5.R ├── get_normalized_data_of_psites.R ├── get_substrate_expr_df.R ├── get_summary_from_ksea.R ├── get_summary_with_unique_sites.R ├── get_unique_AAs_i_df.R ├── keep_psites_with_max_in_topX.R ├── load_data_with_ftp.R ├── load_data_with_http.R ├── mea_based_on_background.R ├── merge_profiling_file_from_Firmiana.R ├── motif_data_frame_to_sequence.R ├── norm_based_on_proteomics_maxquant.R ├── norm_maxquant.R ├── normalize_nopair_ctrl_by_col.R ├── normalize_nopair_noctrl_by_colmed.R ├── normalize_phos_data_to_profiling.R ├── normalize_to_Pair.R ├── plot_seqlogo.R ├── pre_process_filter_psites.R ├── qc_maxquant.R ├── seach_motif_pattern.R ├── visualization_deps_with_scatter.R ├── visualization_fuzzycluster.R ├── visualization_with_simple_pca.R ├── visualization_with_simple_tsne.R ├── visualization_with_umap.R └── write_csv_pep_seq_conf.R ├── README.md ├── doc ├── PhosMap_1.0.0.pdf ├── introduction_of_PhosMap.R ├── introduction_of_PhosMap.Rmd └── introduction_of_PhosMap.html ├── inst ├── .DS_Store ├── extdata │ ├── .DS_Store │ ├── fasta_library │ │ ├── .DS_Store │ │ ├── refseq │ │ │ ├── human │ │ │ │ └── README.txt │ │ │ ├── mouse │ │ │ │ └── README.txt │ │ │ └── rattus │ │ │ │ └── README.txt │ │ └── uniprot │ │ │ ├── human │ │ │ └── README.txt │ │ │ ├── mouse │ │ │ └── README.txt │ │ │ └── rattus │ │ │ └── README.txt │ ├── id_coversion_table │ │ └── README.txt │ ├── kinase_substrate_regulation_relationship_table │ │ ├── .DS_Store │ │ ├── human │ │ │ └── human_ksrr.csv │ │ ├── mouse │ │ │ └── mouse_ksrr.csv │ │ └── rat │ │ │ └── rat_ksrr.csv │ └── motif_library │ │ ├── .DS_Store │ │ ├── refseq │ │ ├── human │ │ │ └── README.txt │ │ ├── mouse │ │ │ └── README.txt │ │ └── rattus │ │ │ └── README.txt │ │ └── uniprot │ │ ├── human │ │ └── README.txt │ │ ├── mouse │ │ └── README.txt │ │ └── rattus │ │ └── README.txt └── src │ └── XMLParser_mascot_dat.py ├── man ├── analysis_deps_anova.Rd ├── analysis_deps_limma.Rd ├── analysis_deps_sam.Rd ├── check_mea_input.Rd ├── compute_kses.Rd ├── construct_pwm.Rd ├── extract_psites_score.Rd ├── fore_seq_to_motif.Rd ├── formatted_output_mef_results.Rd ├── generate_psites_score_file.Rd ├── get_aligned_seq_for_mea.Rd ├── get_colors_for_discrete_value.Rd ├── get_combined_data_frame.Rd ├── get_df_with_AAs_i.Rd ├── get_file_info_from_dir.Rd ├── get_file_suffix.Rd ├── get_filtered_df.Rd ├── get_foreground_df_to_motifs.Rd ├── get_foreground_seq_to_motifs.Rd ├── get_global_background_df.Rd ├── get_ka_by_mean_or_mlr.Rd ├── get_ksea_regulons_info.Rd ├── get_ksea_result_list.Rd ├── get_kses.Rd ├── get_list_with_filtered_sites.Rd ├── get_merged_phospho_df.Rd ├── get_modification_index.Rd ├── get_motif_analysis_summary.Rd ├── get_motifs_list.Rd ├── get_normalized_data_FOT5.Rd ├── get_normalized_data_of_psites.Rd ├── get_substrate_expr_df.Rd ├── get_summary_from_ksea.Rd ├── get_summary_with_unique_sites.Rd ├── get_unique_AAs_i_df.Rd ├── keep_psites_with_max_in_topX.Rd ├── load_data_with_ftp.Rd ├── load_data_with_http.Rd ├── mea_based_on_background.Rd ├── merge_profiling_file_from_Firmiana.Rd ├── motif_data_frame_to_sequence.Rd ├── norm_based_on_proteomics_maxquant.Rd ├── norm_maxquant.Rd ├── normalize_nopair_ctrl_by_col.Rd ├── normalize_nopair_noctrl_by_colmed.Rd ├── normalize_phos_data_to_profiling.Rd ├── normalize_to_Pair.Rd ├── plot_seqlogo.Rd ├── pre_process_filter_psites.Rd ├── qc_maxquant.Rd ├── seach_motif_pattern.Rd ├── visualization_deps_with_scatter.Rd ├── visualization_fuzzycluster.Rd ├── visualization_with_simple_pca.Rd ├── visualization_with_simple_tsne.Rd ├── visualization_with_umap.Rd └── write_csv_pep_seq_conf.Rd └── vignettes ├── .DS_Store └── introduction_of_PhosMap.Rmd /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecnuzdd/PhosMap/HEAD/.DS_Store -------------------------------------------------------------------------------- /.Rbuildignore: -------------------------------------------------------------------------------- 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