vignettes/request_functions.Rmd
request_functions.Rmd“Request functions” is series functions that could be used to request one specific compound/pathway information using web crawler.
BIGG modelis a knowledge base of genome-scale metabolic network reconstructions.
Get the BIGG model information.
dim(x)
#> [1] 108 5
head(x)
#> bigg_id gene_count reaction_count
#> 1 e_coli_core 137 95
#> 2 iAB_RBC_283 346 469
#> 3 iAF1260 1261 2382
#> 4 iAF1260b 1261 2388
#> 5 iAF692 692 690
#> 6 iAF987 987 1285
#> organism metabolite_count
#> 1 Escherichia coli str. K-12 substr. MG1655 72
#> 2 Homo sapiens 342
#> 3 Escherichia coli str. K-12 substr. MG1655 1668
#> 4 Escherichia coli str. K-12 substr. MG1655 1668
#> 5 Methanosarcina barkeri str. Fusaro 628
#> 6 Geobacter metallireducens GS-15 1109Get the BIGG universal metabolite information.
dim(x)
#> [1] 9088 3
head(x)
#> bigg_id name model_bigg_id
#> 1 10fthf 10-Formyltetrahydrofolate Universal
#> 2 10fthf5glu 10-formyltetrahydrofolate-[Glu](5) Universal
#> 3 10fthf6glu 10-formyltetrahydrofolate-[Glu](6) Universal
#> 4 10fthf7glu 10-formyltetrahydrofolate-[Glu](7) Universal
#> 5 10fthfglu__L 10-Formyltetrahydrofolyl L-glutamate Universal
#> 6 10m3ouACP 10-methyl-3-oxo-undecanoyl-ACP UniversalGet one specific metabolite information.
x <-
request_bigg_universal_metabolite(metabolite_id = "g3p",
return_form = "list")
names(x)
#> [1] "bigg_id" "name" "formula"
#> [4] "old_identifiers" "charges" "database_link"
#> [7] "compartments_in_models"
x$database_link
#> database
#> 1 InChI Key
#> 2 Reactome Compound
#> 3 SEED Compound
#> 4 CHEBI
#> 5 Human Metabolome Database
#> 6 MetaNetX (MNX) Chemical
#> 7 KEGG Compound
#> 8 BioCyc
#> id
#> 1 LXJXRIRHZLFYRP-VKHMYHEASA-L
#> 2 29578
#> 3 cpd00102{}cpd19005
#> 4 12983{}12984{}14333{}17138{}181{}18324{}21026{}29052{}5446{}58027{}59776
#> 5 HMDB01112
#> 6 MNXM74
#> 7 C00118{}C00661
#> 8 META:GAPGet universal reaction information.
x <-
request_bigg_universal_reaction_info()
dim(x)
#> [1] 28302 3
head(x)
#> bigg_id name model_bigg_id
#> 1 10FTHF5GLUtl 5-glutamyl-10FTHF transport, lysosomal Universal
#> 2 10FTHF5GLUtm 5-glutamyl-10FTHF transport, mitochondrial Universal
#> 3 10FTHF6GLUtl 6-glutamyl-10FTHF transport, lysosomal Universal
#> 4 10FTHF6GLUtm 6-glutamyl-10FTHF transport, mitochondrial Universal
#> 5 10FTHF7GLUtl 7-glutamyl-10FTHF transport, lysosomal Universal
#> 6 10FTHF7GLUtm 7-glutamyl-10FTHF transport, mitochondrial UniversalGet one specific reaction information.
x <-
request_bigg_universal_reaction(reaction_id = "ADA",
return_form = "list")
names(x)
#> [1] "models_containing_reaction" "bigg_id"
#> [3] "old_identifiers" "pseudoreaction"
#> [5] "name" "reaction_string"
#> [7] "metabolites" "database_link"
x$reaction_string
#> [1] "adn_c + h_c + h2o_c ⇌ ins_c + nh4_c"Get BIGG model version.
request_bigg_version()
#> name value
#> 1 api_version v2
#> 2 last_updated 2019-10-31 10:05:54.157598
#> 3 bigg_models_version 1.6.0Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
Get one specific ChEBI compound information.
x <-
request_chebi_compound(compound_id = "CHEBI:18358")
#> Can't find CHEBI:18358, check it.
names(x)
#> NULL
x$base_info
#> NULLFooDB is the world’s largest and most comprehensive resource on food constituents, chemistry and biology.
Get the FooDB compound information.
x <-
request_foodb_compound_info()
dim(x)
#> [1] 70477 2
head(x)
#> # A tibble: 6 × 2
#> public_id name
#> <chr> <chr>
#> 1 FDB000004 Cyanidin 3-(6''-acetyl-galactoside)
#> 2 FDB000013 Cyanidin 3-(6''-succinyl-glucoside)
#> 3 FDB000014 Pelargonidin 3-(6''-succinyl-glucoside)
#> 4 FDB000024 Petunidin 3-O-(6''-acetyl-galactoside)
#> 5 FDB000025 Peonidin 3-(6''-acetyl-galactoside)
#> 6 FDB000027 Malvidin 3-(6''-acetyl-galactoside)Get one specific FooDB compound information.
x <-
request_foodb_compound(compound_id = "FDB000004",
return_form = "list")
names(x)
#> [1] "version" "creation_date"
#> [3] "update_date" "accession"
#> [5] "name" "description"
#> [7] "synonyms" "chemical_formula"
#> [9] "average_molecular_weight" "monisotopic_moleculate_weight"
#> [11] "iupac_name" "traditional_iupac"
#> [13] "cas_registry_number" "smiles"
#> [15] "inchi" "inchikey"
#> [17] "taxonomy" "state"
#> [19] "predicted_properties" "experimental_properties"
#> [21] "property" "property"
#> [23] "property" "property"
#> [25] "property" "property"
#> [27] "property" "property"
#> [29] "property" "property"
#> [31] "property" "property"
#> [33] "property" "property"
#> [35] "property" "property"
#> [37] "property" "property"
#> [39] "pathways" "spectra"
#> [41] "hmdb_id" "pubchem_compound_id"
#> [43] "chemspider_id" "kegg_id"
#> [45] "chebi_id" "biocyc_id"
#> [47] "het_id" "wikipidia"
#> [49] "vmh_id" "fbonto_id"
#> [51] "foodb_id" "general_references"
#> [53] "foods" "flavors"
#> [55] "enzymes" "health_effects"
x[1:5]
#> $version
#> [1] "1.0"
#>
#> $creation_date
#> [1] "2010-04-08 22:04:24 UTC"
#>
#> $update_date
#> [1] "2020-02-24 19:10:06 UTC"
#>
#> $accession
#> [1] "FDB000004"
#>
#> $name
#> [1] "Cyanidin 3-(6''-acetyl-galactoside)"Get one specific FooDB compound MS2 spectrum.
x <-
request_foodb_compound_ms2(compound_id = "FDB000004")
names(x)
#> [1] "81423" "81424" "81425" "142524" "142525" "142526" "2851882"
#> [8] "2851883" "2851884"
x$`142524`
#> $ms1_info
#> # A tibble: 11 × 2
#> name value
#> <chr> <chr>
#> 1 FooDB ID: FDB000004
#> 2 Compound name: Cyanidin 3-(6''-acetyl-galactoside)
#> 3 Spectrum type: Predicted LC-MS/MS Spectrum - 10V, Ne…
#> 4 Splash Key: splash10-0a4l-9210700000-23f63bb28c350…
#> 5 Notes: This is a predicted spectrum and it sh…
#> 6 Ionization Mode: Negative
#> 7 Collision Energy: 10 eV
#> 8 Instrument Type: QTOF (generic), spectrum predicted by …
#> 9 Mass Resolution: 0.0001 Da
#> 10 Molecular Formula: C23H23O12
#> 11 Molecular Weight (Monoisotopic Mass): 491.119 Da
#>
#> $ms2
#> mz intensity
#> 1 41.00274 2.2712585
#> 2 56.99765 1.3493753
#> 3 59.01330 36.0867255
#> 4 61.02895 0.4772187
#> 5 73.02895 1.8244056
#> 6 85.02895 0.6617838
#> 7 87.00822 1.2406194
#> 8 87.04460 0.2924005
#> 9 89.02387 1.1362507
#> 10 101.02387 0.3326091
#> 11 115.03952 1.0180289
#> 12 117.05517 0.1893737
#> 13 131.03443 1.7830503
#> 14 133.05008 0.1808313
#> 15 145.05008 2.5273298
#> 16 147.06573 0.2993511
#> 17 161.04500 0.5519008
#> 18 175.06065 2.0087344
#> 19 177.07630 0.4475123
#> 20 191.05556 0.7799503
#> 21 193.07121 0.2345258
#> 22 203.05556 0.7035936
#> 23 221.06613 4.8577382
#> 24 341.16003 0.1849506
#> 25 343.17568 0.1849506
#> 26 345.19133 0.1849506
#> 27 371.17059 0.2094764
#> 28 373.18624 0.2094764
#> 29 375.20189 0.2094764
#> 30 489.23359 3.5132804
#> 31 490.11113 34.0488705The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body.
Get one specific HMDB compound information.
x <-
request_hmdb_metabolite(metabolite_id = "HMDB0000001",
return_form = "list")
names(x)
#> [1] "version" "creation_date"
#> [3] "update_date" "accession"
#> [5] "status" "secondary_accessions"
#> [7] "name" "description"
#> [9] "synonyms" "chemical_formula"
#> [11] "average_molecular_weight" "monisotopic_molecular_weight"
#> [13] "iupac_name" "traditional_iupac"
#> [15] "cas_registry_number" "smiles"
#> [17] "inchi" "inchikey"
#> [19] "taxonomy" "ontology"
#> [21] "state" "experimental_properties"
#> [23] "predicted_properties" "spectra"
#> [25] "biological_properties" "normal_concentrations"
#> [27] "abnormal_concentrations" "diseases"
#> [29] "chemspider_id" "drugbank_id"
#> [31] "foodb_id" "pubchem_compound_id"
#> [33] "pdb_id" "chebi_id"
#> [35] "phenol_explorer_compound_id" "knapsack_id"
#> [37] "kegg_id" "biocyc_id"
#> [39] "bigg_id" "wikipedia_id"
#> [41] "metlin_id" "vmh_id"
#> [43] "fbonto_id" "synthesis_reference"
#> [45] "general_references" "protein_associations"
head(x)
#> $version
#> [1] "5.0"
#>
#> $creation_date
#> [1] "2005-11-16 15:48:42 UTC"
#>
#> $update_date
#> [1] "2022-07-12 16:50:58 UTC"
#>
#> $accession
#> [1] "HMDB0000001"
#>
#> $status
#> [1] "quantified"
#>
#> $secondary_accessions
#> $secondary_accessions$accession
#> [1] "HMDB00001"
#>
#> $secondary_accessions$accession
#> [1] "HMDB0004935"
#>
#> $secondary_accessions$accession
#> [1] "HMDB0006703"
#>
#> $secondary_accessions$accession
#> [1] "HMDB0006704"
#>
#> $secondary_accessions$accession
#> [1] "HMDB04935"
#>
#> $secondary_accessions$accession
#> [1] "HMDB06703"
#>
#> $secondary_accessions$accession
#> [1] "HMDB06704"KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
Get all KEGG compound information.
x <-
request_kegg_compound_info()
dim(x)
#> [1] 18929 2
head(x)
#> KEGG.ID
#> 1 C00001
#> 2 C00002
#> 3 C00003
#> 4 C00004
#> 5 C00005
#> 6 C00006
#> Synonyms
#> 1 H2O; Water
#> 2 ATP; Adenosine 5'-triphosphate
#> 3 NAD+; NAD; Nicotinamide adenine dinucleotide; DPN; Diphosphopyridine nucleotide; Nadide; beta-NAD+
#> 4 NADH; DPNH; Reduced nicotinamide adenine dinucleotide
#> 5 NADPH; TPNH; Reduced nicotinamide adenine dinucleotide phosphate
#> 6 NADP+; NADP; Nicotinamide adenine dinucleotide phosphate; beta-Nicotinamide adenine dinucleotide phosphate; TPN; Triphosphopyridine nucleotide; beta-NADP+Get one specific KEGG compound information.
x <-
request_kegg_compound("C02886", "list")
names(x)
#> [1] "ENTRY" "NAME" "FORMULA" "EXACT_MASS" "MOL_WEIGHT"
#> [6] "DBLINKS" "ATOM" "BOND"
x
#> $ENTRY
#> Compound
#> "C02886"
#>
#> $NAME
#> [1] "S-Hexyl-glutathione;" "S-Hexyl-L-glutathione"
#>
#> $FORMULA
#> [1] "C16H29N3O6S"
#>
#> $EXACT_MASS
#> [1] "391.1777"
#>
#> $MOL_WEIGHT
#> [1] "391.483"
#>
#> $DBLINKS
#> [1] "CAS: 24425-56-7" "PubChem: 5817" "ChEBI: 27704"
#> [4] "PDB-CCD: GTX LEE" "NIKKAJI: J394.269D"
#>
#> $ATOM
#> [1] "26" "1 C6a C 20.4431 -14.8878"
#> [3] "2 O6a O 19.2714 -14.2083" "3 O6a O 20.4493 -16.1764"
#> [5] "4 C1c C 27.4860 -14.8878" "5 C5a C 28.6642 -14.2083"
#> [7] "6 N1b N 26.3143 -14.2083" "7 C1b C 27.5110 -16.4896"
#> [9] "8 O5a O 28.6642 -12.8560" "9 C5a C 25.1363 -14.8878"
#> [11] "10 S2a S 26.2084 -17.2437" "11 C1b C 23.9645 -14.2083"
#> [13] "12 O5a O 25.1363 -16.1764" "13 C1b C 26.2084 -18.6025"
#> [15] "14 C1b C 22.7929 -14.8878" "15 C1b C 25.0367 -19.2818"
#> [17] "16 C1c C 21.6148 -14.2083" "17 C1b C 23.8586 -18.6025"
#> [19] "18 N1a N 21.6148 -12.8560" "19 C1b C 22.6868 -19.2818"
#> [21] "20 C1b C 21.5152 -18.6025" "21 C1a C 20.3371 -19.2818"
#> [23] "22 N1b N 29.8424 -14.9100" "23 C1b C 31.0549 -14.2100"
#> [25] "24 C6a C 32.2673 -14.9100" "25 O6a O 33.4797 -14.2100"
#> [27] "26 O6a O 32.2673 -16.3100"
#>
#> $BOND
#> [1] "25" "1 1 2 1" "2 1 3 2"
#> [4] "3 4 5 1" "4 4 6 1" "5 4 7 1 #Down"
#> [7] "6 5 8 2" "7 6 9 1" "8 7 10 1"
#> [10] "9 9 11 1" "10 9 12 2" "11 10 13 1"
#> [13] "12 11 14 1" "13 13 15 1" "14 14 16 1"
#> [16] "15 15 17 1" "16 16 18 1 #Up" "17 17 19 1"
#> [19] "18 19 20 1" "19 20 21 1" "20 5 22 1"
#> [22] "21 22 23 1" "22 23 24 1" "23 24 25 1"
#> [25] "24 24 26 2" "25 1 16 1"Get all KEGG drug information.
x <-
request_kegg_drug_info()
dim(x)
#> [1] 11934 2
head(x)
#> KEGG.ID
#> 1 D00001
#> 2 D00002
#> 3 D00003
#> 4 D00004
#> 5 D00005
#> 6 D00006
#> Synonyms
#> 1 Water (JP18/USP); Purified water (JP18); Purified water in containers (JP18); Water, purified (USP); Sterile purified water in containers (JP18); Water for injection (JP18); Water for injection in containers (JP18); Sterile water (TN)
#> 2 Nadide (JAN/USAN/INN); Nicotinamide adenine dinucleotide
#> 3 Oxygen (JP18/USP)
#> 4 Carbon dioxide (JP18/USP); Carbon dioxide (TN)
#> 5 Flavin adenine dinucleotide (JAN); Adeflavin (TN)
#> 6 Pyridoxal phosphate hydrate (JP18); Pyridoxal phosphate monohydrate; Hipyridoxin (TN)Get one specific KEGG drug information.
x <-
request_kegg_drug("D00001", "list")
names(x)
#> [1] "ENTRY" "NAME" "PRODUCT" "FORMULA" "EXACT_MASS"
#> [6] "MOL_WEIGHT" "REMARK" "EFFICACY" "BRITE" "DBLINKS"
#> [11] "ATOM" "BOND"
x
#> $ENTRY
#> Drug
#> "D00001"
#>
#> $NAME
#> [1] "Water (JP18/USP);"
#> [2] "Purified water (JP18);"
#> [3] "Purified water in containers (JP18);"
#> [4] "Water, purified (USP);"
#> [5] "Sterile purified water in containers (JP18);"
#> [6] "Water for injection (JP18);"
#> [7] "Water for injection in containers (JP18);"
#> [8] "Sterile water (TN)"
#>
#> $PRODUCT
#> $PRODUCT$PRODUCT
#> [1] "BACTERIOSTATIC WATER (HF Acquisition Co LLC) 99b0ef9b-600a-40dc-e053-2a95a90aa07e"
#> [2] "BACTERIOSTATIC WATER (Hospira) 87d6e9dc-fe3b-4593-ac9a-d7493d1959c7"
#> [3] "BACTERIOSTATIC WATER (REMEDYREPACK) b8f88bab-c914-4ad2-a096-363d57147948"
#> [4] "STERILE WATER (B. Braun Medical) d99f9133-e4d0-4dee-b611-dbc3f918b547"
#> [5] "STERILE WATER (HF Acquisition Co LLC) 7610bf80-61b7-982f-e053-2a91aa0ac1bb"
#> [6] "STERILE WATER (HF Acquisition Co LLC) 77bd3c0f-f4ab-7cfa-e053-2a91aa0a1b83"
#> [7] "STERILE WATER (HF Acquisition Co LLC) 99b1cb12-0b2d-0c0f-e053-2a95a90ac3b6"
#> [8] "STERILE WATER (HF Acquisition Co. LLC) 74ed2a6f-824c-a1ff-e053-2a91aa0a57c0"
#> [9] "STERILE WATER (A-S Medication Solutions) dba87371-31d2-47c2-ab83-89aabce4b184"
#> [10] "STERILE WATER (Asclemed USA) 45c38269-883c-4198-a9d5-03810a4420ec"
#> [11] "STERILE WATER (B. Braun Medical) 8924e52e-8622-4ed6-a061-1908183e0a18"
#> [12] "STERILE WATER (B. Braun Medical) 8fc8d87a-3951-4ac5-97df-c161ffc90475"
#> [13] "STERILE WATER (B. Braun Medical) f4284eb6-e553-46d4-90d8-efc80a90a480"
#> [14] "STERILE WATER (Baxter Healthcare Company) 210dc9ab-d6ca-4552-ac19-1be17792d290"
#> [15] "STERILE WATER (Baxter Healthcare Company) 8bcf5572-49e1-4302-9522-56f57904cb4a"
#> [16] "STERILE WATER (Baxter Healthcare Corporation) ef3e79c5-3f58-4b36-a296-64b7d9a651c1"
#> [17] "STERILE WATER (Cardinal Health) 9655cd02-82b5-4a75-813b-854b19551481"
#> [18] "BACTERIOSTATIC WATER (General Injectables & Vaccine) 21eadcab-0f74-4d3f-9bcc-6cf7e260fdd0"
#> [19] "STERILE WATER (General Injectables & Vaccines) c6eed2ad-25f3-479e-9c28-1945eea88f8d"
#> [20] "STERILE WATER (General Injectables and Vaccines) a82d2dd5-dd65-4208-ab85-f0680d0e2bf6"
#> [21] "STERILE WATER (Henry Schein) 88403fcf-a276-42c0-88b6-bd84a720b564"
#> [22] "BACTERIOSTATIC WATER (Henry Schein) a833502e-a622-4e81-8c58-cef6ccb6c4c9"
#> [23] "STERILE WATER (Henry Schein) f4087143-9868-4308-b96c-43657ee8ec28"
#> [24] "STERILE WATER (Hospira) 1fe046e2-d6e1-413a-a59c-4ea2a4841c79"
#> [25] "STERILE WATER (Hospira) 2b9ea23a-f9e9-48a8-25b7-519e3bbd6828"
#> [26] "STERILE WATER (ICU Medical) 1c0bbcb7-5ed6-4ee7-b297-080d3359474e"
#> [27] "STERILE WATER (ICU Medical) aab10f03-26ae-4dbc-a481-ef025e48b405"
#> [28] "STERILE WATER (ICU Medical) e3484bc6-ed7f-43ef-9d49-c131a8dff2dd"
#> [29] "BACTERIOSTATIC WATER (Medical Purchasing Solutions) 69485218-9343-952d-e053-2a91aa0ad4e8"
#> [30] "STERILE WATER (Medical Purchasing Solutions) 81a1a49e-fd89-59d8-e053-2a91aa0ac3c3"
#> [31] "STERILE WATER (Medical Purchasing Solutions) 9c9851b6-2702-e893-e053-2a95a90a729c"
#>
#> $PRODUCT$GENERIC
#> [1] "STERILE WATER (Nephron Pharmaceuticals Corporation) bc04a883-babc-87a6-e053-2995a90a3dfd"
#> [2] "STERILE WATER (Medefil) 99e99a50-82d5-aff6-e053-2a95a90a8c56"
#> [3] "STERILE WATER (Civica) 3f49eedf-5bf5-4a95-b704-c956d860ca04"
#> [4] "STERILE WATER (Fresenius Kabi USA) b45e9f1d-9c48-4b46-8541-d846b89540df"
#> [5] "STERILE WATER (Fresenius Kabi USA) e71c6c83-d518-496c-b2ab-efd5987e4783"
#> [6] "STERILE WATER (Hikma Pharmaceuticals USA) 78ef7ad3-451d-43d0-a9b6-5cf0aadca003"
#>
#>
#> $FORMULA
#> [1] "H2O"
#>
#> $EXACT_MASS
#> [1] "18.0106"
#>
#> $MOL_WEIGHT
#> [1] "18.0153"
#>
#> $REMARK
#> [1] "Same as: C00001"
#> [2] "Therapeutic category: 7131"
#> [3] "Product: D00001<JP/US>"
#> [4] "Product (mixture): D05352<JP> D05354<JP> D06417<JP>"
#>
#> $EFFICACY
#> [1] "Pharmaceutic aid (solvent)"
#>
#> $BRITE
#> [1] "Therapeutic category of drugs in Japan [BR:br08301]"
#> [2] " 7 Agents not mainly for therapeutic purpose"
#> [3] " 71 Dispensing medicines"
#> [4] " 713 Solvents"
#> [5] " 7131 Purified water"
#> [6] " D00001 Water (JP18/USP); Purified water (JP18); Purified water in containers (JP18); Water, purified (USP); Sterile purified water in containers (JP18); Water for injection (JP18); Water for injection in containers (JP18)"
#> [7] "Risk category of Japanese OTC drugs [BR:br08312]"
#> [8] " Third-class OTC drugs"
#> [9] " Inorganic and organic chemicals"
#> [10] " Water"
#> [11] " D00001 Water (JP18/USP)"
#> [12] "Drugs listed in the Japanese Pharmacopoeia [BR:br08311]"
#> [13] " Chemicals"
#> [14] " D00001 Water"
#> [15] " D00001 Purified water"
#> [16] " D00001 Purified water in containers"
#> [17] " D00001 Sterile purified Water in containers"
#> [18] " D00001 Water for injection"
#> [19] " D00001 Sterile water for injection in containers"
#>
#> $DBLINKS
#> [1] "CAS: 7732-18-5" "PubChem: 7847069" "ChEBI: 15377"
#> [4] "PDB-CCD: HOH O" "LigandBox: D00001" "NIKKAJI: J43.587B"
#>
#> $ATOM
#> [1] "1" "1 O0 O 32.0259 -17.5852"
#>
#> $BOND
#> [1] "0"Get all KEGG reaction class (rclass) information.
x <-
request_kegg_rclass_info()
dim(x)
#> [1] 3180 2
head(x)
#> KEGG.ID name
#> 1 RC00001 C1x-C8x:*-*:C2x+C2y-C8x+C8y N1y-N5y:*-*:C1y+C2x+C2x-C1y+C8x+C8x
#> 2 RC00002 O1c-O2c:*-P1b:P1b-P1b
#> 3 RC00003 S0-S2a:C1a-*:C1b+C1b-C1b+C1b
#> 4 RC00004 S1a-S2a:*-C5a:C1b-C1b
#> 5 RC00005 O1c-O2b:*-C1y:P1b-P1b
#> 6 RC00006 C1c-C5a:N1a+*-*+O5a:C1b+C6a-C1b+C6aGet one specific KEGG reaction information.
x <-
request_kegg_reaction(reaction_id = "R00001")
names(x)
#> [1] "ENTRY" "NAME" "DEFINITION" "EQUATION" "ENZYME"
#> [6] "DBLINKS"
x
#> $ENTRY
#> Reaction
#> "R00001"
#>
#> $NAME
#> [1] "polyphosphate polyphosphohydrolase"
#>
#> $DEFINITION
#> [1] "Polyphosphate + n H2O <=> (n+1) Oligophosphate"
#>
#> $EQUATION
#> [1] "C00404 + n C00001 <=> (n+1) C02174"
#>
#> $ENZYME
#> [1] "3.6.1.10"
#>
#> $DBLINKS
#> [1] "RHEA: 22455"Get all pathway information.
x <-
request_kegg_pathway_info(organism = "hsa")
dim(x)
#> [1] 347 2
head(x)
#> KEGG.ID Pathway.name
#> 1 hsa00010 Glycolysis / Gluconeogenesis - Homo sapiens (human)
#> 2 hsa00020 Citrate cycle (TCA cycle) - Homo sapiens (human)
#> 3 hsa00030 Pentose phosphate pathway - Homo sapiens (human)
#> 4 hsa00040 Pentose and glucuronate interconversions - Homo sapiens (human)
#> 5 hsa00051 Fructose and mannose metabolism - Homo sapiens (human)
#> 6 hsa00052 Galactose metabolism - Homo sapiens (human)Get one specific pathway information.
x <-
request_kegg_pathway(pathway_id = "hsa00010")
names(x)
#> [1] "ENTRY" "NAME" "DESCRIPTION" "CLASS" "PATHWAY_MAP"
#> [6] "MODULE" "NETWORK" "DRUG" "DBLINKS" "ORGANISM"
#> [11] "GENE" "COMPOUND" "REL_PATHWAY" "KO_PATHWAY" "REFERENCE"
x
#> $ENTRY
#> Pathway
#> "hsa00010"
#>
#> $NAME
#> [1] "Glycolysis / Gluconeogenesis - Homo sapiens (human)"
#>
#> $DESCRIPTION
#> [1] "Glycolysis is the process of converting glucose into pyruvate and generating small amounts of ATP (energy) and NADH (reducing power). It is a central pathway that produces important precursor metabolites: six-carbon compounds of glucose-6P and fructose-6P and three-carbon compounds of glycerone-P, glyceraldehyde-3P, glycerate-3P, phosphoenolpyruvate, and pyruvate [MD:M00001]. Acetyl-CoA, another important precursor metabolite, is produced by oxidative decarboxylation of pyruvate [MD:M00307]. When the enzyme genes of this pathway are examined in completely sequenced genomes, the reaction steps of three-carbon compounds from glycerone-P to pyruvate form a conserved core module [MD:M00002], which is found in almost all organisms and which sometimes contains operon structures in bacterial genomes. Gluconeogenesis is a synthesis pathway of glucose from noncarbohydrate precursors. It is essentially a reversal of glycolysis with minor variations of alternative paths [MD:M00003]."
#>
#> $CLASS
#> [1] "Metabolism; Carbohydrate metabolism"
#>
#> $PATHWAY_MAP
#> hsa00010
#> "Glycolysis / Gluconeogenesis"
#>
#> $MODULE
#> hsa_M00001
#> "Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:hsa00010]"
#> hsa_M00002
#> "Glycolysis, core module involving three-carbon compounds [PATH:hsa00010]"
#> hsa_M00003
#> "Gluconeogenesis, oxaloacetate => fructose-6P [PATH:hsa00010]"
#> hsa_M00307
#> "Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:hsa00010]"
#>
#> $NETWORK
#> $NETWORK$NETWORK
#> [1] "nt06017 Glycogen metabolism"
#>
#> $NETWORK$ELEMENT
#> [1] "N00731 Glycolysis"
#>
#>
#> $DRUG
#> [1] "D00123" "Cyanamide (JP18)"
#> [3] "D00131" "Disulfiram (JP18/USP/INN)"
#> [5] "D07257" "Lonidamine (INN)"
#> [7] "D08970" "Piragliatin (USAN)"
#> [9] "D11342" "Dorzagliatin (USAN)"
#> [11] "D11408" "Mitapivat sulfate (USAN)"
#> [13] "D12320" "Cadisegliatin (USAN)"
#> [15] "D12362" "Etavopivat (USAN/INN)"
#>
#> $DBLINKS
#> [1] "GO: 0006096 0006094"
#>
#> $ORGANISM
#> Homo sapiens (human) [GN:hsa]
#> "NA Homo sapiens (human) [GN:hsa]"
#>
#> $GENE
#> [1] "3101"
#> [2] "HK3; hexokinase 3 [KO:K00844] [EC:2.7.1.1]"
#> [3] "3098"
#> [4] "HK1; hexokinase 1 [KO:K00844] [EC:2.7.1.1]"
#> [5] "3099"
#> [6] "HK2; hexokinase 2 [KO:K00844] [EC:2.7.1.1]"
#> [7] "80201"
#> [8] "HKDC1; hexokinase domain containing 1 [KO:K00844] [EC:2.7.1.1]"
#> [9] "2645"
#> [10] "GCK; glucokinase [KO:K12407] [EC:2.7.1.2]"
#> [11] "2821"
#> [12] "GPI; glucose-6-phosphate isomerase [KO:K01810] [EC:5.3.1.9]"
#> [13] "5213"
#> [14] "PFKM; phosphofructokinase, muscle [KO:K00850] [EC:2.7.1.11]"
#> [15] "5214"
#> [16] "PFKP; phosphofructokinase, platelet [KO:K00850] [EC:2.7.1.11]"
#> [17] "5211"
#> [18] "PFKL; phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]"
#> [19] "2203"
#> [20] "FBP1; fructose-bisphosphatase 1 [KO:K03841] [EC:3.1.3.11]"
#> [21] "8789"
#> [22] "FBP2; fructose-bisphosphatase 2 [KO:K03841] [EC:3.1.3.11]"
#> [23] "230"
#> [24] "ALDOC; aldolase, fructose-bisphosphate C [KO:K01623] [EC:4.1.2.13]"
#> [25] "226"
#> [26] "ALDOA; aldolase, fructose-bisphosphate A [KO:K01623] [EC:4.1.2.13]"
#> [27] "229"
#> [28] "ALDOB; aldolase, fructose-bisphosphate B [KO:K01623] [EC:4.1.2.13]"
#> [29] "7167"
#> [30] "TPI1; triosephosphate isomerase 1 [KO:K01803] [EC:5.3.1.1]"
#> [31] "2597"
#> [32] "GAPDH; glyceraldehyde-3-phosphate dehydrogenase [KO:K00134] [EC:1.2.1.12]"
#> [33] "26330"
#> [34] "GAPDHS; glyceraldehyde-3-phosphate dehydrogenase, spermatogenic [KO:K10705] [EC:1.2.1.12]"
#> [35] "5232"
#> [36] "PGK2; phosphoglycerate kinase 2 [KO:K00927] [EC:2.7.2.3]"
#> [37] "5230"
#> [38] "PGK1; phosphoglycerate kinase 1 [KO:K00927] [EC:2.7.2.3]"
#> [39] "5223"
#> [40] "PGAM1; phosphoglycerate mutase 1 [KO:K01834] [EC:5.4.2.11]"
#> [41] "5224"
#> [42] "PGAM2; phosphoglycerate mutase 2 [KO:K01834] [EC:5.4.2.11]"
#> [43] "441531"
#> [44] "PGAM4; phosphoglycerate mutase family member 4 [KO:K01834] [EC:5.4.2.11]"
#> [45] "2027"
#> [46] "ENO3; enolase 3 [KO:K01689] [EC:4.2.1.11]"
#> [47] "2026"
#> [48] "ENO2; enolase 2 [KO:K01689] [EC:4.2.1.11]"
#> [49] "2023"
#> [50] "ENO1; enolase 1 [KO:K01689] [EC:4.2.1.11]"
#> [51] "387712"
#> [52] "ENO4; enolase 4 [KO:K01689] [EC:4.2.1.11]"
#> [53] "5315"
#> [54] "PKM; pyruvate kinase M1/2 [KO:K00873] [EC:2.7.1.40]"
#> [55] "5313"
#> [56] "PKLR; pyruvate kinase L/R [KO:K12406] [EC:2.7.1.40]"
#> [57] "5161"
#> [58] "PDHA2; pyruvate dehydrogenase E1 subunit alpha 2 [KO:K00161] [EC:1.2.4.1]"
#> [59] "5160"
#> [60] "PDHA1; pyruvate dehydrogenase E1 subunit alpha 1 [KO:K00161] [EC:1.2.4.1]"
#> [61] "5162"
#> [62] "PDHB; pyruvate dehydrogenase E1 subunit beta [KO:K00162] [EC:1.2.4.1]"
#> [63] "1737"
#> [64] "DLAT; dihydrolipoamide S-acetyltransferase [KO:K00627] [EC:2.3.1.12]"
#> [65] "1738"
#> [66] "DLD; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]"
#> [67] "160287"
#> [68] "LDHAL6A; lactate dehydrogenase A like 6A [KO:K00016] [EC:1.1.1.27]"
#> [69] "92483"
#> [70] "LDHAL6B; lactate dehydrogenase A like 6B [KO:K00016] [EC:1.1.1.27]"
#> [71] "3939"
#> [72] "LDHA; lactate dehydrogenase A [KO:K00016] [EC:1.1.1.27]"
#> [73] "3945"
#> [74] "LDHB; lactate dehydrogenase B [KO:K00016] [EC:1.1.1.27]"
#> [75] "3948"
#> [76] "LDHC; lactate dehydrogenase C [KO:K00016] [EC:1.1.1.27]"
#> [77] "124"
#> [78] "ADH1A; alcohol dehydrogenase 1A (class I), alpha polypeptide [KO:K13951] [EC:1.1.1.1]"
#> [79] "125"
#> [80] "ADH1B; alcohol dehydrogenase 1B (class I), beta polypeptide [KO:K13951] [EC:1.1.1.1]"
#> [81] "126"
#> [82] "ADH1C; alcohol dehydrogenase 1C (class I), gamma polypeptide [KO:K13951] [EC:1.1.1.1]"
#> [83] "131"
#> [84] "ADH7; alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide [KO:K13951] [EC:1.1.1.1]"
#> [85] "127"
#> [86] "ADH4; alcohol dehydrogenase 4 (class II), pi polypeptide [KO:K13980] [EC:1.1.1.1]"
#> [87] "128"
#> [88] "ADH5; alcohol dehydrogenase 5 (class III), chi polypeptide [KO:K00121] [EC:1.1.1.284 1.1.1.1]"
#> [89] "130"
#> [90] "ADH6; alcohol dehydrogenase 6 (class V) [KO:K13952] [EC:1.1.1.1]"
#> [91] "10327"
#> [92] "AKR1A1; aldo-keto reductase family 1 member A1 [KO:K00002] [EC:1.1.1.2]"
#> [93] "217"
#> [94] "ALDH2; aldehyde dehydrogenase 2 family member [KO:K00128] [EC:1.2.1.3]"
#> [95] "224"
#> [96] "ALDH3A2; aldehyde dehydrogenase 3 family member A2 [KO:K00128] [EC:1.2.1.3]"
#> [97] "219"
#> [98] "ALDH1B1; aldehyde dehydrogenase 1 family member B1 [KO:K00128] [EC:1.2.1.3]"
#> [99] "501"
#> [100] "ALDH7A1; aldehyde dehydrogenase 7 family member A1 [KO:K14085] [EC:1.2.1.31 1.2.1.8 1.2.1.3]"
#> [101] "223"
#> [102] "ALDH9A1; aldehyde dehydrogenase 9 family member A1 [KO:K00149] [EC:1.2.1.47 1.2.1.3]"
#> [103] "221"
#> [104] "ALDH3B1; aldehyde dehydrogenase 3 family member B1 [KO:K00129] [EC:1.2.1.5]"
#> [105] "222"
#> [106] "ALDH3B2; aldehyde dehydrogenase 3 family member B2 [KO:K00129] [EC:1.2.1.5]"
#> [107] "218"
#> [108] "ALDH3A1; aldehyde dehydrogenase 3 family member A1 [KO:K00129] [EC:1.2.1.5]"
#> [109] "84532"
#> [110] "ACSS1; acyl-CoA synthetase short chain family member 1 [KO:K01895] [EC:6.2.1.1]"
#> [111] "55902"
#> [112] "ACSS2; acyl-CoA synthetase short chain family member 2 [KO:K01895] [EC:6.2.1.1]"
#> [113] "130589"
#> [114] "GALM; galactose mutarotase [KO:K01785] [EC:5.1.3.3]"
#> [115] "5236"
#> [116] "PGM1; phosphoglucomutase 1 [KO:K01835] [EC:5.4.2.2]"
#> [117] "55276"
#> [118] "PGM2; phosphoglucomutase 2 [KO:K15779] [EC:5.4.2.2 5.4.2.7]"
#> [119] "2538"
#> [120] "G6PC1; glucose-6-phosphatase catalytic subunit 1 [KO:K01084] [EC:3.1.3.9]"
#> [121] "57818"
#> [122] "G6PC2; glucose-6-phosphatase catalytic subunit 2 [KO:K01084] [EC:3.1.3.9]"
#> [123] "92579"
#> [124] "G6PC3; glucose-6-phosphatase catalytic subunit 3 [KO:K01084] [EC:3.1.3.9]"
#> [125] "83440"
#> [126] "ADPGK; ADP dependent glucokinase [KO:K08074] [EC:2.7.1.147]"
#> [127] "669"
#> [128] "BPGM; bisphosphoglycerate mutase [KO:K01837] [EC:5.4.2.4 5.4.2.11]"
#> [129] "9562"
#> [130] "MINPP1; multiple inositol-polyphosphate phosphatase 1 [KO:K03103] [EC:3.1.3.62 3.1.3.80]"
#> [131] "5105"
#> [132] "PCK1; phosphoenolpyruvate carboxykinase 1 [KO:K01596] [EC:4.1.1.32]"
#> [133] "5106"
#> [134] "PCK2; phosphoenolpyruvate carboxykinase 2, mitochondrial [KO:K01596] [EC:4.1.1.32]"
#>
#> $COMPOUND
#> C00022
#> "Pyruvate"
#> C00024
#> "Acetyl-CoA"
#> C00031
#> "D-Glucose"
#> C00033
#> "Acetate"
#> C00036
#> "Oxaloacetate"
#> C00068
#> "Thiamin diphosphate"
#> C00074
#> "Phosphoenolpyruvate"
#> C00084
#> "Acetaldehyde"
#> C00103
#> "D-Glucose 1-phosphate"
#> C00111
#> "Glycerone phosphate"
#> C00118
#> "D-Glyceraldehyde 3-phosphate"
#> C00186
#> "(S)-Lactate"
#> C00197
#> "3-Phospho-D-glycerate"
#> C00221
#> "beta-D-Glucose"
#> C00236
#> "3-Phospho-D-glyceroyl phosphate"
#> C00267
#> "alpha-D-Glucose"
#> C00469
#> "Ethanol"
#> C00631
#> "2-Phospho-D-glycerate"
#> C00668
#> "alpha-D-Glucose 6-phosphate"
#> C01159
#> "2,3-Bisphospho-D-glycerate"
#> C01172
#> "beta-D-Glucose 6-phosphate"
#> C01451
#> "Salicin"
#> C05125
#> "2-(alpha-Hydroxyethyl)thiamine diphosphate"
#> C05345
#> "beta-D-Fructose 6-phosphate"
#> C05378
#> "beta-D-Fructose 1,6-bisphosphate"
#> C06186
#> "Arbutin"
#> C06187
#> "Arbutin 6-phosphate"
#> C06188
#> "Salicin 6-phosphate"
#> C15972
#> "Enzyme N6-(lipoyl)lysine"
#> C15973
#> "Enzyme N6-(dihydrolipoyl)lysine"
#> C16255
#> "[Dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine"
#>
#> $REL_PATHWAY
#> hsa00020 hsa00030
#> "Citrate cycle (TCA cycle)" "Pentose phosphate pathway"
#> hsa00500 hsa00620
#> "Starch and sucrose metabolism" "Pyruvate metabolism"
#> hsa00640
#> "Propanoate metabolism"
#>
#> $KO_PATHWAY
#> [1] "ko00010"
#>
#> $REFERENCE
#> $REFERENCE[[1]]
#> $REFERENCE[[1]]$REFERENCE
#> [1] ""
#>
#> $REFERENCE[[1]]$AUTHORS
#> [1] "Nishizuka Y (ed)."
#>
#> $REFERENCE[[1]]$TITLE
#> [1] "[Metabolic Maps] (In Japanese)"
#>
#> $REFERENCE[[1]]$JOURNAL
#> [1] "Tokyo Kagaku Dojin (1980)"
#>
#>
#> $REFERENCE[[2]]
#> $REFERENCE[[2]]$REFERENCE
#> [1] ""
#>
#> $REFERENCE[[2]]$AUTHORS
#> [1] "Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds)."
#>
#> $REFERENCE[[2]]$TITLE
#> [1] "[Cellular Functions and Metabolic Maps] (In Japanese)"
#>
#> $REFERENCE[[2]]$JOURNAL
#> [1] "Tokyo Kagaku Dojin (1997)"
#>
#>
#> $REFERENCE[[3]]
#> $REFERENCE[[3]]$REFERENCE
#> [1] ""
#>
#> $REFERENCE[[3]]$AUTHORS
#> [1] "Michal G."
#>
#> $REFERENCE[[3]]$TITLE
#> [1] "Biochemical Pathways"
#>
#> $REFERENCE[[3]]$JOURNAL
#> [1] "Wiley (1999)"The official database of Japanese Conference on the Biochemistry of Lipids (JCBL). Link
Get the LipidBank lipid class.
x <-
request_lipidbank_lipid_class(lipid_class = "Wax")
#> Check your internet.
dim(x)
#> NULL
head(x)
#> NULLLIPID MAPS Lipidomics Gateway was created in 2003 via an NIH “Glue Grant” to provide access to lipid nomenclature, databases, tools, protocols, standards, tutorials, meetings, publications, and other resources and serving the international lipid research community.
Get one specific lipid information.
x <-
request_lipidmaps_lipid(lipid_id = "LMFA01030001")
x
#> Synonyms
#> 2 5Z,8Z,11Z,14Z-icosatetraenoic acid{}AA{}Arachidonate{}cis-5,8,11,14-Eicosatetraenoic acid{}(all-Z)-5,8,11,14-Eicosatetraenoic acid{}all-cis-5,8,11,14-Eicosatetraenoic acid
#> Common_Name Systematic_Name LM_ID Status
#> 2 Arachidonic acid 5Z,8Z,11Z,14Z-eicosatetraenoic acid LMFA01030001 Active
#> Exact_Mass Formula Abbrev Category
#> 2 304.2402 C20H32O2 FA 20:4 Fatty Acyls [FA]
#> Main.Class Sub.Class
#> 2 Fatty Acids and Conjugates [FA01] Unsaturated fatty acids [FA0103]
#> InChiKey
#> 2 YZXBAPSDXZZRGB-DOFZRALJSA-N
#> InChi
#> 2 InChI=1S/C20H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20(21)22/h6-7,9-10,12-13,15-16H,2-5,8,11,14,17-19H2,1H3,(H,21,22)/b7-6-,10-9-,13-12-,16-15-
#> SMILES Curated.from
#> 2 C(O)(=O)CCC/C=C\\C/C=C\\C/C=C\\C/C=C\\CCCCC Homo sapiens (#9606)
#> NCBI.taxonomy.class Wikipedia KEGG.ID HMDB.ID CHEBI.ID
#> 2 Mammalia (#40674) Arachidonic acid C00219 HMDB0001043 15843
#> LIPIDBANK.ID PubChem.CID PlantFA.ID SwissLipids.ID Cayman.ID NA.
#> 2 DFA0213 444899 10144 SLM:000000296 10007268 <NA>We can also get information from WikiPedia.
Get one specific compound information.
x <-
request_wikipedia_compound(compound_id = "Microcystin-LR")
dim(x)
#> [1] 36 2
head(x)
#> # A tibble: 6 × 2
#> name value
#> <chr> <chr>
#> 1 "Names" "Nam…
#> 2 "IUPAC name\n(5R,8S,11R,12S,15S,18S,19S,22R)-15-[3-(diaminomethylidenea… "IUP…
#> 3 "Other names\n5-L-Arginine-microcystin LA" "Oth…
#> 4 "Identifiers" "Ide…
#> 5 "CAS Number" "101…
#> 6 "3D model (JSmol)" "Int…Get the classification of one species
x <-
request_wikipedia_scientific_classification(species_id = "Aaptos ciliata")
dim(x)
#> [1] 7 2
x
#> name value
#> 1 Kingdom Animalia
#> 2 Phylum Porifera
#> 3 Class Demospongiae
#> 4 Order Suberitida
#> 5 Family Suberitidae
#> 6 Genus Aaptos
#> 7 Species A. ciliata
sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur ... 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] massdatabase_0.99.14
#>
#> loaded via a namespace (and not attached):
#> [1] readxl_1.4.0 circlize_0.4.15
#> [3] systemfonts_1.0.4 selectr_0.4-2
#> [5] igraph_1.3.2 plyr_1.8.7
#> [7] lazyeval_0.2.2 BiocParallel_1.30.3
#> [9] listenv_0.8.0 ChemmineR_3.48.0
#> [11] GenomeInfoDb_1.32.2 ggplot2_3.3.6
#> [13] Rdisop_1.56.0 digest_0.6.29
#> [15] foreach_1.5.2 yulab.utils_0.0.5
#> [17] htmltools_0.5.2 viridis_0.6.2
#> [19] massdataset_1.0.5 fansi_1.0.3
#> [21] magrittr_2.0.3 memoise_2.0.1
#> [23] metpath_0.99.4 cluster_2.1.3
#> [25] doParallel_1.0.17 tzdb_0.3.0
#> [27] openxlsx_4.2.5 limma_3.52.2
#> [29] graphlayouts_0.8.0 readr_2.1.2
#> [31] ComplexHeatmap_2.12.0 globals_0.15.1
#> [33] Biostrings_2.64.0 matrixStats_0.62.0
#> [35] pkgdown_2.0.5 prettyunits_1.1.1
#> [37] colorspace_2.0-3 ggrepel_0.9.1
#> [39] rvest_1.0.2 metid_1.2.15
#> [41] textshaping_0.3.6 xfun_0.31
#> [43] dplyr_1.0.9 crayon_1.5.1
#> [45] RCurl_1.98-1.7 jsonlite_1.8.0
#> [47] impute_1.70.0 iterators_1.0.14
#> [49] glue_1.6.2 polyclip_1.10-0
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