Files in egmg726/crisscrosslinker
An R package for protein interaction analysis
DESCRIPTION
NAMESPACE
R/blast.menuOptions.R
R/blastMenu.R
R/generate_2d_pdb_file.R
R/get_pdb_info.R
R/get_pwa_ranges.R
R/get_pwa_strings.R
R/importedFunctions.R
R/make_pdb_menu_options.R
R/pdb_functions2.R
R/ppi.alignPDB.R
R/ppi.combineData.R
R/ppi.distAnalysis.R
R/ppi.loadData.R
R/ppi.matchPDB.R
R/ppi.matchPDB2.R
R/ppi.matchPDB3.R
R/ppi.matchUniprot.R
R/ppi.pymol.R
R/rbd.alignBS.R
R/rbd.alignBS2.R
R/rbd.find_new_pattern.R
R/rbd.freqVector.R
R/rbd.getBSfromDF.R
R/rbd.getBSfromIET.R
R/rbd.getBindingSeq.R
R/rbd.getBindingSeq3.R
R/rbd.xinet.R
R/rdb.pymol.R
R/renumber_and_identify_missing_aa.R
R/uniprot.PDBmap.R
R/uniprotfasta.R
README.md
data/bs_output_repeats_pdb.RData
data/bs_output_repeats_uniprot.RData
data/chimera_colors.RData
data/pymol_color_table.RData
data/rbdmapData.RData
data/xlink.df.filt.pdb.RData
data/xlink.df.uniprot.RData
images/ccl_hex.jpeg
images/crisscrosslinker_logo.png
inst/extdata/NSMB_FASTA/PRC2_5m.fasta
inst/extdata/NSMB_FASTA/PRC2_5m_Uniprot.fasta
inst/extdata/NSMB_RBDmap/Repeat01_NoXL_ArgC_eluate.txt
inst/extdata/NSMB_RBDmap/Repeat01_NoXL_ArgC_input.txt
inst/extdata/NSMB_RBDmap/Repeat01_NoXL_LysC_eluate.txt
inst/extdata/NSMB_RBDmap/Repeat01_NoXL_LysC_input.txt
inst/extdata/NSMB_RBDmap/Repeat01_UV_ArgC_eluate.txt
inst/extdata/NSMB_RBDmap/Repeat01_UV_ArgC_input.txt
inst/extdata/NSMB_RBDmap/Repeat01_UV_LysC_eluate.txt
inst/extdata/NSMB_RBDmap/Repeat01_UV_LysC_input.txt
inst/extdata/NSMB_RBDmap/Repeat02_NoXL_ArgC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat02_NoXL_ArgC_input_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat02_NoXL_LysC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat02_NoXL_LysC_input_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat02_UV_ArgC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat02_UV_ArgC_input_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat02_UV_LysC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat02_UV_LysC_input_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat03_NoXL_ArgC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat03_NoXL_ArgC_input_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat03_NoXL_LysC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat03_NoXL_LysC_input_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat03_UV_ArgC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat03_UV_ArgC_input_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat03_UV_LysC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat03_UV_LysC_input_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat04_NoXL_ArgC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat04_NoXL_ArgC_input_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat04_NoXL_LysC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat04_NoXL_LysC_input_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat04_UV_ArgC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat04_UV_ArgC_input_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat04_UV_LysC_eluate_MaxQuant_txt.txt
inst/extdata/NSMB_RBDmap/Repeat04_UV_LysC_input_MaxQuant_txt.txt
inst/extdata/NSMB_XLMS/PRC2-AEBP2 _4.xlsx
inst/extdata/NSMB_XLMS/PRC2-AEBP2_1.xlsx
inst/extdata/NSMB_XLMS/PRC2-AEBP2_2.xlsx
inst/extdata/NSMB_XLMS/PRC2-AEBP2_3.xlsx
inst/extdata/NSMB_XLMS/PRC2-AEBP2_5.xlsx
inst/extdata/NSMB_XLMS/PRC2-AEBP2_6.csv
inst/extdata/NSMB_XLMS/PRC2-AEBP2_7.csv
inst/extdata/NSMB_XLMS/PRC2-MTF2-EPOP_1.xlsx
inst/extdata/NSMB_XLMS/PRC2-MTF2-EPOP_2.csv
inst/extdata/NSMB_XLMS/PRC2-PHF19_1.xlsx
inst/extdata/NSMB_XLMS/PRC2-PHF19_2.xlsx
inst/extdata/NSMB_XLMS/PRC2-PHF19_3.xlsx
inst/extdata/NSMB_XLMS/PRC2-PHF19_4.csv
inst/extdata/NSMB_misc/PRC2_alternative_dict.csv
inst/extdata/NSMB_misc/PRC2_protein_dict.csv
inst/extdata/RBDmap/data.txt
inst/extdata/RNAPolII_ppi/Sample.fasta
inst/extdata/RNAPolII_ppi/Sample_Cross-linked_peptides.csv
inst/extdata/RNAPolII_ppi/Sample_alignIDs.csv
inst/extdata/RNAPolII_ppi/Sample_loop-linked_peptides.csv
man/blast.menu.Rd
man/blast.menuOptions.Rd
man/bs_output_repeats_pdb.Rd
man/bs_output_repeats_pdb2.Rd
man/bs_output_repeats_uniprot.Rd
man/check_download_read_pdb.Rd
man/color.pymol.Rd
man/consolidate_resno_and_resid.Rd
man/display_preferred_pdb_structure_menu.Rd
man/do_sr_chain_loop.Rd
man/fasta.combine.Rd
man/firstup.Rd
man/generate_2d_pdb_file.Rd
man/generate_pdb_lists_from_pdb_csv.Rd
man/get_missing_amino_acids.Rd
man/get_pdb_info.Rd
man/get_pwa_ranges.Rd
man/get_pwa_strings.Rd
man/get_resno_and_resid.Rd
man/get_uniprot_info_from_proteins_api.Rd
man/get_vector_of_distances_by_pos_freq.Rd
man/get_xyz_coordinates_pdb.Rd
man/get_xyz_min_max.Rd
man/go_through_menu_loops.Rd
man/is.sequential.Rd
man/load_proxl_data.Rd
man/make_binding_site_df.Rd
man/make_binding_site_rows_for_supp_df.Rd
man/make_intensity_output_df.Rd
man/make_pdb_menu_options.Rd
man/make_plink2_master_list.Rd
man/make_proteins_and_intensity_list_from_pipeline_output.Rd
man/make_renumbered_pdb_vectors.Rd
man/make_start_end_pdb_df_output2.Rd
man/make_uv_xlms_visualization.Rd
man/ppi.alignPDB.Rd
man/ppi.analyze.Rd
man/ppi.combineData.Rd
man/ppi.distAnalysis.Rd
man/ppi.freqCount.Rd
man/ppi.loadData.Rd
man/ppi.matchPDB.Rd
man/ppi.matchPDB2.Rd
man/ppi.matchPDB3.Rd
man/ppi.matchUniprot.Rd
man/ppi.pymol.Rd
man/ppi.xinet.Rd
man/pymol_color_table.Rd
man/quick_pwa_from_pdb.Rd
man/quick_resno_and_resid.Rd
man/rbd.alignBS.Rd
man/rbd.alignBS2.Rd
man/rbd.freqVector.Rd
man/rbd.getBSfromDF.Rd
man/rbd.getBSfromIET.Rd
man/rbd.getBindingSeq.Rd
man/rbd.getBindingSeq3.Rd
man/rbd.makeIEPlot.Rd
man/rbd.makeIETable.Rd
man/rbd.makeSeqHitList.Rd
man/rbd.menuDBSearch.Rd
man/rbd.pymol.Rd
man/rbd.xinet.Rd
man/renumber_and_identify_missing_aa.Rd
man/renumber_binding_site_df_from_uniprot_fasta.Rd
man/split_sequences.Rd
man/split_sequences2.Rd
man/uniprot.PDBmap.Rd
man/uniprot.fasta.Rd
man/xlink.df.filt.pdb.Rd
man/xlink.df.uniprot.Rd
tutorials/crisscross_BS3_tutorial_script.R
tutorials/crisscross_RBDMap_tutorial_script.R
tutorials/nsmb_pipeline_ppi.Rmd
tutorials/nsmb_pipeline_rbdmap.Rmd
