Files in ecnuzdd/PhosMap
A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data
.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
Meta/vignette.rds
NAMESPACE
NEWS
PhosMap.Rproj
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
doc/introduction_of_PhosMap.html
inst/.DS_Store
inst/extdata/.DS_Store
inst/extdata/fasta_library/.DS_Store
inst/extdata/fasta_library/refseq/human/README.txt
inst/extdata/fasta_library/refseq/mouse/README.txt
inst/extdata/fasta_library/refseq/rattus/README.txt
inst/extdata/fasta_library/uniprot/human/README.txt
inst/extdata/fasta_library/uniprot/mouse/README.txt
inst/extdata/fasta_library/uniprot/rattus/README.txt
inst/extdata/id_coversion_table/README.txt
inst/extdata/kinase_substrate_regulation_relationship_table/.DS_Store
inst/extdata/kinase_substrate_regulation_relationship_table/human/human_ksrr.csv
inst/extdata/kinase_substrate_regulation_relationship_table/mouse/mouse_ksrr.csv
inst/extdata/kinase_substrate_regulation_relationship_table/rat/rat_ksrr.csv
inst/extdata/motif_library/.DS_Store
inst/extdata/motif_library/refseq/human/README.txt
inst/extdata/motif_library/refseq/mouse/README.txt
inst/extdata/motif_library/refseq/rattus/README.txt
inst/extdata/motif_library/uniprot/human/README.txt
inst/extdata/motif_library/uniprot/mouse/README.txt
inst/extdata/motif_library/uniprot/rattus/README.txt
inst/src/XMLParser_mascot_dat.py
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/.DS_Store
vignettes/introduction_of_PhosMap.Rmd
