Files in momeara/BioChemPantry

Load bioinformatics datasets into a local database

.gitignore

0_load_drugbank_xml.R 1_parse_drugbank_xml.R

DESCRIPTION

LICENSE

NAMESPACE

R/id_utils.R R/pantry.R R/quality_tests.R R/r_utils.R R/uniprot.R README.md man/create_schema.Rd man/date_code.Rd man/drop_schema.Rd man/drop_table.Rd man/get_pantry.Rd man/get_pantry_config.Rd man/get_schema.Rd man/get_schemas.Rd man/get_search_path.Rd man/get_staging_directory.Rd man/get_tables.Rd man/make_symmetric.Rd man/schema_tbl.Rd man/set_schema.Rd man/summarize_map.Rd man/test_distinct.Rd man/test_is_symmetric.Rd man/test_null_count.Rd man/test_null_frac.Rd man/uniprot_entry_web_lookup.Rd man/uniprot_taxa.Rd man/uniprot_web_lookup.Rd

vignette/COVID19/raw_data/2020-03-18_Krogan_SARSCoV2_27baits.xlsx

vignette/COVID19/raw_data/2020-03-18_Krogan_SARSCoV2_27baits_LowThreshold.xlsx

vignette/COVID19/scripts/1_read_nCov_host_ppi.R vignette/COVID19/scripts/2_merge_chembl.R vignette/COVID19/scripts/2_merge_iuphar.R vignette/COVID19/scripts/2_merge_uniprot.R vignette/COVID19/scripts/README.md vignette/COVID19/scripts/uniprot.R

vignette/sets/chembl21/.gitignore

vignette/sets/chembl21/doc/README.txt

vignette/sets/chembl21/scripts/0_load_chembl_database.R vignette/sets/chembl21/scripts/1_zinc_to_chembl.R vignette/sets/chembl21/scripts/2_chembl_target_classes.R vignette/sets/chembl21/scripts/3_target_info.R vignette/sets/chembl21/scripts/4__activity_types.R vignette/sets/chembl21/scripts/4_chembl_db_export.R vignette/sets/chembl21/scripts/5.1_make_sea_library_count_based_fingerprint.R vignette/sets/chembl21/scripts/5_make_sea_library.R vignette/sets/chembl21/scripts/6.1_random_matrix_theory.R vignette/sets/chembl21/scripts/6_compute_sea_networks.R vignette/sets/chembl21/scripts/7_save_to_db.R vignette/sets/chembl21/scripts/8_blastp.R

vignette/sets/chembl21/scripts/extract_fingerprints.py

vignette/sets/chembl21/scripts/make_seaware_background.py

vignette/sets/chembl21/scripts/sea-wrapper.sh

vignette/sets/chembl22/doc/README.txt

vignette/sets/chembl22/fpcore.cfg

vignette/sets/chembl22/scripts/0_load_chembl_database.R vignette/sets/chembl22/scripts/1_zinc_to_chembl.R vignette/sets/chembl22/scripts/2_chembl_target_classes.R vignette/sets/chembl22/scripts/3_target_info.R vignette/sets/chembl22/scripts/4__activity_types.R vignette/sets/chembl22/scripts/4_chembl_db_export.R vignette/sets/chembl22/scripts/5.1_make_sea_library_count_based_fingerprint.R vignette/sets/chembl22/scripts/5_make_sea_library.R vignette/sets/chembl22/scripts/6_compute_sea_networks.R vignette/sets/chembl22/scripts/7_save_to_db.R vignette/sets/chembl22/scripts/8_blastp.R

vignette/sets/chembl22/scripts/make_seaware_background.py

vignette/sets/chembl22/scripts/sea-wrapper.sh

vignette/sets/chembl23/README.txt

vignette/sets/chembl23/dir.cfg

vignette/sets/chembl23/fpcore.cfg

vignette/sets/chembl23/scripts/0_load_chembl_database.R vignette/sets/chembl23/scripts/1_zinc_to_chembl.R vignette/sets/chembl23/scripts/2_chembl_target_classes.R vignette/sets/chembl23/scripts/3_target_info.R vignette/sets/chembl23/scripts/4__activity_types.R vignette/sets/chembl23/scripts/4_chembl_db_export.R vignette/sets/chembl23/scripts/5.1_make_sea_library_count_based_fingerprint.R vignette/sets/chembl23/scripts/5_make_sea_library.R vignette/sets/chembl23/scripts/6_compute_sea_networks.R vignette/sets/chembl23/scripts/7_save_to_db.R vignette/sets/chembl23/scripts/8_blastp.R vignette/sets/chembl23/scripts/hit_lead_background_model/0_compute_compound_vs_compound_similarities.R vignette/sets/chembl23/scripts/hit_lead_background_model/1_sample_background.R vignette/sets/chembl23/scripts/hit_lead_background_model/2_analyze_target_set_correlation.R

vignette/sets/chembl23/scripts/hit_lead_background_model/compute_target_set_correlation.py

vignette/sets/chembl23/scripts/hit_lead_background_model/hit_to_lead.cpp

vignette/sets/chembl23/scripts/make_seaware_background.py

vignette/sets/chembl23/scripts/sea-wrapper.sh

vignette/sets/chembl24/README.txt

vignette/sets/chembl24/dir.cfg

vignette/sets/chembl24/fpcore.cfg

vignette/sets/chembl24/scripts/0_load_chembl_database.R vignette/sets/chembl24/scripts/1_zinc_to_chembl.R vignette/sets/chembl24/scripts/2_chembl_target_classes.R vignette/sets/chembl24/scripts/3_target_info.R vignette/sets/chembl24/scripts/4__activity_types.R vignette/sets/chembl24/scripts/4_chembl_db_export.R vignette/sets/chembl24/scripts/5.1_make_sea_library_count_based_fingerprint.R vignette/sets/chembl24/scripts/5_make_sea_library.R vignette/sets/chembl24/scripts/6_compute_sea_networks.R vignette/sets/chembl24/scripts/7_save_to_db.R vignette/sets/chembl24/scripts/8_blastp.R vignette/sets/chembl24/scripts/hit_lead_background_model/0_compute_compound_vs_compound_similarities.R vignette/sets/chembl24/scripts/hit_lead_background_model/1_sample_background.R vignette/sets/chembl24/scripts/hit_lead_background_model/2_analyze_target_set_correlation.R

vignette/sets/chembl24/scripts/hit_lead_background_model/compute_target_set_correlation.py

vignette/sets/chembl24/scripts/hit_lead_background_model/hit_to_lead.cpp

vignette/sets/chembl24/scripts/make_seaware_background.py

vignette/sets/chembl24/scripts/parameters.R

vignette/sets/chembl24/scripts/sea-wrapper.sh

vignette/sets/csfmetabolome/scripts/0_collect_data.R vignette/sets/csfmetabolome/scripts/1_parse_metabolites_xml.R

vignette/sets/gencode/gencode24/.gitignore

vignette/sets/gencode/gencode24/scripts/1_load_gencode.R

vignette/sets/gencode/gencode27/.gitignore

vignette/sets/gencode/gencode27/scripts/1_load_gencode.R vignette/sets/guide_to_pharmacology/scripts/1_load_data.R vignette/sets/guide_to_pharmacology/scripts/gpcr_targets.R vignette/sets/guide_to_pharmacology/scripts/metabolic_code.R

vignette/sets/hgnc/release_160324/.gitignore

vignette/sets/hgnc/release_160324/scripts/1_load_data.R vignette/sets/hgnc/release_160324/scripts/2_blast_human_proteins_vs_human_proteins.R vignette/sets/hgnc/release_160324/scripts/3_load_orthologs.R

vignette/sets/hgnc/release_171217/.gitignore

vignette/sets/hgnc/release_171217/scripts/1_load_data.R vignette/sets/hgnc/release_171217/scripts/2_blast_human_proteins_vs_human_proteins.R vignette/sets/hgnc/release_171217/scripts/2_gene_families.R vignette/sets/hgnc/release_171217/scripts/3_load_orthologs.R vignette/sets/hmdb/scripts/0_download_metabolites_xml.R vignette/sets/hmdb/scripts/1.1_parse_hmdb_concentration_xml.R vignette/sets/hmdb/scripts/1_parse_hmdb_metabolites_xml.R vignette/sets/hmdb/scripts/2_load_data.R

vignette/sets/pfam30/.gitignore

vignette/sets/pfam30/scripts/1_load_pfam.R

vignette/sets/pfam31/*R*

vignette/sets/pfam31/.gitignore

vignette/sets/pfam31/scripts/1_load_pfam.R vignette/sets/uniprot/scripts/1_download.R vignette/sets/uniprot/scripts/2_load_idmapping.R vignette/sets/uniprot/scripts/3_load_fasta.R

momeara/BioChemPantry documentation built on Aug. 13, 2021, 9:46 p.m.