Man pages for egmg726/crisscrosslinker
An R package for protein interaction analysis
| blast.menu | BLAST sequence and go through menu loops |
| blast.menuOptions | Make PDB Menu Options |
| bs_output_repeats_pdb | Processed PRC2 RBDmap Data aligned to PDB |
| bs_output_repeats_pdb2 | Processed PRC2 RBDmap Data aligned to PDB |
| bs_output_repeats_uniprot | Processed PRC2 RBDmap Data aligned to Uniprot |
| check_download_read_pdb | Check Download Read PDB |
| color.pymol | Color PyMol |
| consolidate_resno_and_resid | Consolidate resno_and_resid |
| display_preferred_pdb_structure_menu | Display Preferred PDB Structure Menu |
| do_sr_chain_loop | Match query sequence to chain in PDB file |
| fasta.combine | Combine FASTA files |
| firstup | Capitalize first letter |
| generate_2d_pdb_file | Generate 2D PDB File |
| generate_pdb_lists_from_pdb_csv | Generate PDB Lists from PDB CSV |
| get_missing_amino_acids | Get missing amino acids/fragments |
| get_pdb_info | Get PDB Info |
| get_pwa_ranges | Get ranges from pairwise alignment results |
| get_pwa_strings | Get string from pairwise alignment results |
| get_resno_and_resid | Get resno and resid from chain in pdb_read |
| get_uniprot_info_from_proteins_api | get uniprot info from proteins api |
| get_vector_of_distances_by_pos_freq | Get Vector of Distances by Position Frequency |
| get_xyz_coordinates_pdb | Get XYZ coordinates from PDB file |
| get_xyz_min_max | Get min and max of xyz coordinates |
| go_through_menu_loops | BLAST sequence and go through menu loops |
| is.sequential | Is Sequential |
| load_proxl_data | Load ProXL Data |
| make_binding_site_df | Make binding site dataframe |
| make_binding_site_rows_for_supp_df | make_binding_site_rows_for_supp_df |
| make_intensity_output_df | Make intesnity output dataframe |
| make_pdb_menu_options | Make PDB Menu Options |
| make_plink2_master_list | Make pLink2 master list |
| make_proteins_and_intensity_list_from_pipeline_output | Make Proteins and Intensities List |
| make_renumbered_pdb_vectors | Make renumbered PDB vectors |
| make_start_end_pdb_df_output2 | Make start and end csv file for make_diff_analysis function |
| make_uv_xlms_visualization | Make UV XLMS Visualization |
| ppi.alignPDB | PPI Align PDB |
| ppi.analyze | BS3 Differential Analysis Inclusive Function |
| ppi.combineData | PPI: Combine Data |
| ppi.distAnalysis | PPI Distance Analysis |
| ppi.freqCount | Count Frequencies of Sequences in ppi.analyze() output |
| ppi.loadData | PPI: Load Data |
| ppi.matchPDB | PPI: Match PDB |
| ppi.matchPDB2 | PPI Match PDB 2 |
| ppi.matchPDB3 | Match PDB 3 |
| ppi.matchUniprot | PPI: Match Protein Sequences to UniProt |
| ppi.pymol | Write PyMOL file for protein-protein interaction data |
| ppi.xinet | Makes file for xiNET input |
| pymol_color_table | PyMol Colors |
| quick_pwa_from_pdb | Quick PWA from PDB |
| quick_resno_and_resid | resno_and_resid Shortcut Function |
| rbd.alignBS | RBD: Align Binding Sequences to Uniprot and PDB |
| rbd.alignBS2 | RBD: Align Binding Sequences to Uniprot and PDB |
| rbd.freqVector | Get Frequency Vector for RBDmap Data |
| rbd.getBindingSeq | Get Binding Sequence from RBDmap Data - Zhang et. al 2019... |
| rbd.getBindingSeq3 | RBD: Get Binding Sequence - Casetello et. al 2016 Method |
| rbd.getBSfromDF | RBD: Get binding sequences from Dataframe |
| rbd.getBSfromIET | Get Binding Sequences from Input/Eluate Table |
| rbd.makeIEPlot | Make input/eluate plot |
| rbd.makeIETable | Make input and eluate table |
| rbd.makeSeqHitList | Make sequence hit list |
| rbd.menuDBSearch | Menu DB Search |
| rbd.pymol | Write PyMol file for RBDmap Data |
| rbd.xinet | RBDmap: xiNET Output |
| renumber_and_identify_missing_aa | Renumber and identify missing amino acids in pairwise... |
| renumber_binding_site_df_from_uniprot_fasta | Renumber binding site df from uniprot fasta |
| split_sequences | Split Sequences |
| split_sequences2 | Split sequences from plink output |
| uniprot.fasta | Fetch FASTA sequence from Uniprot |
| uniprot.PDBmap | UniProt PDBmap |
| xlink.df.filt.pdb | Processed PRC2 PPI Data aligned to PDB |
| xlink.df.uniprot | Processed PRC2 PPI Data aligned to Uniprot |
