Files in ecnuzdd/PhosMap

A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

R/analysis_deps_anova.R R/analysis_deps_limma.R R/analysis_deps_sam.R R/check_mea_input.R R/compute_kses.R R/construct_pwm.R R/extract_psites_score.R R/fore_seq_to_motif.R R/formatted_output_mef_results.R R/generate_psites_score_file.R R/get_aligned_seq_for_mea.R R/get_colors_for_discrete_value.R R/get_combined_data_frame.R R/get_df_with_AAs_i.R R/get_file_info_from_dir.R R/get_file_suffix.R R/get_filtered_df.R R/get_foreground_df_to_motifs.R R/get_foreground_seq_to_motifs.R R/get_global_background_df.R R/get_ka_by_mean_or_mlr.R R/get_ksea_regulons_info.R R/get_ksea_result_list.R R/get_kses.R R/get_list_with_filtered_sites.R R/get_merged_phospho_df.R R/get_modification_index.R R/get_motif_analysis_summary.R R/get_motifs_list.R R/get_normalized_data_FOT5.R R/get_normalized_data_of_psites.R R/get_substrate_expr_df.R R/get_summary_from_ksea.R R/get_summary_with_unique_sites.R R/get_unique_AAs_i_df.R R/keep_psites_with_max_in_topX.R R/load_data_with_ftp.R R/load_data_with_http.R R/mea_based_on_background.R R/merge_profiling_file_from_Firmiana.R R/motif_data_frame_to_sequence.R R/norm_based_on_proteomics_maxquant.R R/norm_maxquant.R R/normalize_nopair_ctrl_by_col.R R/normalize_nopair_noctrl_by_colmed.R R/normalize_phos_data_to_profiling.R R/normalize_to_Pair.R R/plot_seqlogo.R R/pre_process_filter_psites.R R/qc_maxquant.R R/seach_motif_pattern.R R/visualization_deps_with_scatter.R R/visualization_fuzzycluster.R R/visualization_with_simple_pca.R R/visualization_with_simple_tsne.R R/visualization_with_umap.R R/write_csv_pep_seq_conf.R README.md doc/PhosMap_1.0.0.pdf doc/introduction_of_PhosMap.R doc/introduction_of_PhosMap.Rmd man/analysis_deps_anova.Rd man/analysis_deps_limma.Rd man/analysis_deps_sam.Rd man/check_mea_input.Rd man/compute_kses.Rd man/construct_pwm.Rd man/extract_psites_score.Rd man/fore_seq_to_motif.Rd man/formatted_output_mef_results.Rd man/generate_psites_score_file.Rd man/get_aligned_seq_for_mea.Rd man/get_colors_for_discrete_value.Rd man/get_combined_data_frame.Rd man/get_df_with_AAs_i.Rd man/get_file_info_from_dir.Rd man/get_file_suffix.Rd man/get_filtered_df.Rd man/get_foreground_df_to_motifs.Rd man/get_foreground_seq_to_motifs.Rd man/get_global_background_df.Rd man/get_ka_by_mean_or_mlr.Rd man/get_ksea_regulons_info.Rd man/get_ksea_result_list.Rd man/get_kses.Rd man/get_list_with_filtered_sites.Rd man/get_merged_phospho_df.Rd man/get_modification_index.Rd man/get_motif_analysis_summary.Rd man/get_motifs_list.Rd man/get_normalized_data_FOT5.Rd man/get_normalized_data_of_psites.Rd man/get_substrate_expr_df.Rd man/get_summary_from_ksea.Rd man/get_summary_with_unique_sites.Rd man/get_unique_AAs_i_df.Rd man/keep_psites_with_max_in_topX.Rd man/load_data_with_ftp.Rd man/load_data_with_http.Rd man/mea_based_on_background.Rd man/merge_profiling_file_from_Firmiana.Rd man/motif_data_frame_to_sequence.Rd man/norm_based_on_proteomics_maxquant.Rd man/norm_maxquant.Rd man/normalize_nopair_ctrl_by_col.Rd man/normalize_nopair_noctrl_by_colmed.Rd man/normalize_phos_data_to_profiling.Rd man/normalize_to_Pair.Rd man/plot_seqlogo.Rd man/pre_process_filter_psites.Rd man/qc_maxquant.Rd man/seach_motif_pattern.Rd man/visualization_deps_with_scatter.Rd man/visualization_fuzzycluster.Rd man/visualization_with_simple_pca.Rd man/visualization_with_simple_tsne.Rd man/visualization_with_umap.Rd man/write_csv_pep_seq_conf.Rd vignettes/introduction_of_PhosMap.Rmd