Man pages for ecnuzdd/PhosMap
A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data
| analysis_deps_anova | Differential expression analysis using ANOVA |
| analysis_deps_limma | Differential expression analysis using limma. |
| analysis_deps_sam | Differential expression analysis using SAM |
| check_mea_input | Check input for motif enrichment analysis (mea) |
| compute_kses | computing kinase-substrate enrichment score |
| construct_pwm | Construct position weight matrix |
| extract_psites_score | Create R codes to call python for parsering mascot xml. |
| fore_seq_to_motif | Convert the list that consists of motifs and the... |
| formatted_output_mef_results | Output formatted sequences in foreground that are mapped to... |
| generate_psites_score_file | Generate peptide identification files with psites scores. |
| get_aligned_seq_for_mea | Taking S/T/Y as the center, align sequence to fasta library... |
| get_colors_for_discrete_value | Generate custom colors from discrete values for heatmaps. |
| get_combined_data_frame | Get a data frame mapped ID to Gene Symbol. |
| get_df_with_AAs_i | Get a data frame of amino acid sequences for proteins. |
| get_file_info_from_dir | Get data lists from files and the corresponding file ids. |
| get_file_suffix | Get sufffix of input file. |
| get_filtered_df | Get data frame filtered based on the Mascot and reference... |
| get_foreground_df_to_motifs | Get filtered foreground data frame that its aligned sequences... |
| get_foreground_seq_to_motifs | Get motifs and their corresponding aligned sequences form... |
| get_global_background_df | Get background data frame (fasta library from Refseq). |
| get_ka_by_mean_or_mlr | Computing kinase activity using mean value and multiple... |
| get_ksea_regulons_info | Get informational data frame by combining results from all... |
| get_ksea_result_list | Kinase activity analysis based on known and predicted... |
| get_kses | computing kinase-substrate enrichment significance (pvalue) |
| get_list_with_filtered_sites | Filter phosphorylation sites. |
| get_merged_phospho_df | Get merged data frame with phospho-peptides. |
| get_modification_index | Get indexes of modifications in protein sequences. |
| get_motif_analysis_summary | Get summary results of motif analysis for specific input |
| get_motifs_list | Motif enrichment using rmotifx. |
| get_normalized_data_FOT5 | Normailization on basis of sum |
| get_normalized_data_of_psites | To normalize data and filter data only including... |
| get_substrate_expr_df | Get a data frame only containing kinase inferred by KSEA |
| get_summary_from_ksea | Get a data frame only containing inforamtion of kinase... |
| get_summary_with_unique_sites | Assign psites to protein sequence. |
| get_unique_AAs_i_df | Get data frame without redundancy. |
| keep_psites_with_max_in_topX | Keep psites whose row maximum is top N (percentage). |
| load_data_with_ftp | Load datasets from URL... |
| load_data_with_http | Load datasets from URL... |
| mea_based_on_background | Motif enrichment based on global background (fasta library... |
| merge_profiling_file_from_Firmiana | Merge profiling files downloaded from Firmiana. |
| motif_data_frame_to_sequence | Convert data frame of motif to the sequence pattern |
| normalize_nopair_ctrl_by_col | For data without pairs but with control, normalize them to... |
| normalize_nopair_noctrl_by_colmed | For data without pairs and control, normalize them to the... |
| normalize_phos_data_to_profiling | Normalize phospho-data to profiling |
| normalize_to_Pair | For data with pairs, normalize them to the sample with flag... |
| norm_based_on_proteomics_maxquant | Normalizaiton for phosphoproteomics data from MaxQuant based... |
| norm_maxquant | Normalizaiton, imputation and filtering for phosphoproteomics... |
| plot_seqlogo | Plot sequence logo based on list that consist of motifs and... |
| pre_process_filter_psites | Get peptides data frame passed phosphorylation sites quality... |
| qc_maxquant | Quality control for phosphoproteomics data from MaxQuant. |
| seach_motif_pattern | Convert data frame of motif to the sequence pattern |
| visualization_deps_with_scatter | Visualize differentially expressed results with scatter |
| visualization_fuzzycluster | Visualize results from fuzzy clusters with line chart |
| visualization_with_simple_pca | A simple PCA plot. |
| visualization_with_simple_tsne | A simple t-SNE plot. |
| visualization_with_umap | A umap plot. |
| write_csv_pep_seq_conf | Write data to specific direction with CSV format. |
