{ "_id": "6a103f42acfb0bcc41c9ccf1", "Package": "HTGM", "Version": "1.2", "Date": "2025-05-14", "Title": "High Throughput 'GoMiner'", "Authors@R": "c(\nperson(\"Barry\", \"Zeeberg\", email = \"barryz2013@gmail.com\",\nrole = c(\"aut\", \"cre\")))", "Maintainer": "Barry Zeeberg ", "Author": "Barry Zeeberg [aut, cre]", "LazyData": "true", "LazyDataCompression": "xz", "Description": "Two papers published in the early 2000's (Zeeberg, B.R.,\nFeng, W., Wang, G. et al. (2003) )\nand (Zeeberg, B.R., Qin, H., Narashimhan, S., et al. (2005)\n) implement 'GoMiner' and 'High\nThroughput GoMiner' ('HTGM') to map lists of genes to the Gene\nOntology (GO) . Until recently, these\nwere hosted on a server at The National Cancer Institute (NCI).\nIn order to continue providing these services to the\nbio-medical community, I have developed stand-alone versions.\nThe current package 'HTGM' builds upon my recent package\n'GoMiner'. The output of 'GoMiner' is a heatmap showing the\nrelationship of a single list of genes and the significant\ncategories into which they map. 'High Throughput GoMiner'\n('HTGM') integrates the results of the individual 'GoMiner'\nanalyses. The output of 'HTGM' is a heatmap showing the\nrelationship of the significant categories derived from each\ngene list. The heatmap has only 2 axes, so the identity of the\ngenes are unfortunately \"integrated out of the equation.\"\nBecause the graphic for the heatmap is implemented in Scalable\nVector Graphics (SVG) technology, it is relatively easy to\nhyperlink each picture element to the relevant list of genes.\nBy clicking on the desired picture element, the user can\nrecover the \"lost\" genes.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 08:53:16 UTC", "User": "root" }, "Repository": "https://barryzee.r-universe.dev", "Date/Publication": "2025-05-14 17:00:02 UTC", "RemoteUrl": "https://github.com/cran/HTGM", "RemoteRef": "HEAD", "RemoteSha": "e50e6dd91b3cd707fa2108f2f812110978bc829d", "MD5sum": "d4f4126ad881b8123942270d89ad6122", "_user": "barryzee", "_type": "src", "_file": "HTGM_1.2.tar.gz", "_fileid": 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"GoMiner", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "vprint", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 3, "_updates": [ { "week": "2025-20", "n": 1 } ], "_tags": [ { "name": "1.2", "date": "2025-05-14" } ], "_stars": 0, "_contributors": [ { "user": "barryzee", "count": 3, "uuid": 75148535 } ], "_userbio": { "uuid": 75148535, "type": "user", "name": "barryzee" }, "_downloads": { "count": 607, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/HTGM" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HTGM.html", "manual.pdf" ], 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"array" ], "fields": [ "GO_0000028__ribosomal_small_subunit_assembly", "GO_0000209__protein_polyubiquitination", "GO_0000350__generation_of_catalytic_spliceosome_for_second_transesterification_step", "GO_0000381__regulation_of_alternative_mRNA_splicing__via_spliceosome", "GO_0000413__protein_peptidyl-prolyl_isomerization", "GO_0000470__maturation_of_LSU-rRNA", "GO_0001558__regulation_of_cell_growth", "GO_0001967__suckling_behavior", "GO_0002026__regulation_of_the_force_of_heart_contraction", "GO_0002071__glandular_epithelial_cell_maturation", "GO_0002181__cytoplasmic_translation", "GO_0002296__T-helper_1_cell_lineage_commitment", "GO_0002327__immature_B_cell_differentiation", "GO_0002710__negative_regulation_of_T_cell_mediated_immunity", "GO_0003179__heart_valve_morphogenesis", "GO_0006112__energy_reserve_metabolic_process", "GO_0006119__oxidative_phosphorylation", "GO_0006122__mitochondrial_electron_transport__ubiquinol_to_cytochrome_c", "GO_0006207__'de_novo'_pyrimidine_nucleobase_biosynthetic_process", "GO_0006307__DNA_alkylation_repair", "GO_0006334__nucleosome_assembly", "GO_0006352__DNA-templated_transcription_initiation", "GO_0006366__transcription_by_RNA_polymerase_II", "GO_0006397__mRNA_processing", "GO_0006404__RNA_import_into_nucleus", "GO_0006405__RNA_export_from_nucleus", "GO_0006412__translation", "GO_0006413__translational_initiation", "GO_0006415__translational_termination", "GO_0006489__dolichyl_diphosphate_biosynthetic_process", "GO_0006491__N-glycan_processing", "GO_0006606__protein_import_into_nucleus", "GO_0006607__NLS-bearing_protein_import_into_nucleus", "GO_0006610__ribosomal_protein_import_into_nucleus", "GO_0006626__protein_targeting_to_mitochondrion", "GO_0006879__intracellular_iron_ion_homeostasis", "GO_0006886__intracellular_protein_transport", "GO_0006892__post-Golgi_vesicle-mediated_transport", "GO_0006998__nuclear_envelope_organization", "GO_0007034__vacuolar_transport", "GO_0007035__vacuolar_acidification", "GO_0007079__mitotic_chromosome_movement_towards_spindle_pole", "GO_0007165__signal_transduction", "GO_0007617__mating_behavior", "GO_0008333__endosome_to_lysosome_transport", "GO_0008380__RNA_splicing", "GO_0008610__lipid_biosynthetic_process", "GO_0008631__intrinsic_apoptotic_signaling_pathway_in_response_to_oxidative_stress", "GO_0009100__glycoprotein_metabolic_process", "GO_0010614__negative_regulation_of_cardiac_muscle_hypertrophy", "GO_0010800__positive_regulation_of_peptidyl-threonine_phosphorylation", "GO_0010831__positive_regulation_of_myotube_differentiation", "GO_0016024__CDP-diacylglycerol_biosynthetic_process", "GO_0016192__vesicle-mediated_transport", "GO_0016226__iron-sulfur_cluster_assembly", "GO_0016241__regulation_of_macroautophagy", "GO_0016242__negative_regulation_of_macroautophagy", "GO_0019408__dolichol_biosynthetic_process", "GO_0019432__triglyceride_biosynthetic_process", "GO_0019640__D-glucuronate_catabolic_process_to_D-xylulose_5-phosphate", "GO_0022008__neurogenesis", "GO_0023052__signaling", "GO_0030261__chromosome_condensation", "GO_0030307__positive_regulation_of_cell_growth", "GO_0030953__astral_microtubule_organization", "GO_0031087__deadenylation-independent_decapping_of_nuclear-transcribed_mRNA", "GO_0031124__mRNA_3'-end_processing", "GO_0031529__ruffle_organization", "GO_0031670__cellular_response_to_nutrient", "GO_0032383__regulation_of_intracellular_cholesterol_transport", "GO_0032482__Rab_protein_signal_transduction", "GO_0032511__late_endosome_to_vacuole_transport_via_multivesicular_body_sorting_pathway", "GO_0032543__mitochondrial_translation", "GO_0032648__regulation_of_interferon-beta_production", "GO_0032790__ribosome_disassembly", "GO_0032927__positive_regulation_of_activin_receptor_signaling_pathway", "GO_0032957__inositol_trisphosphate_metabolic_process", "GO_0033173__calcineurin-NFAT_signaling_cascade", "GO_0033299__secretion_of_lysosomal_enzymes", "GO_0033674__positive_regulation_of_kinase_activity", "GO_0033962__P-body_assembly", "GO_0034058__endosomal_vesicle_fusion", "GO_0034122__negative_regulation_of_toll-like_receptor_signaling_pathway", "GO_0034123__positive_regulation_of_toll-like_receptor_signaling_pathway", "GO_0034393__positive_regulation_of_smooth_muscle_cell_apoptotic_process", "GO_0034976__response_to_endoplasmic_reticulum_stress", "GO_0035268__protein_mannosylation", "GO_0035435__phosphate_ion_transmembrane_transport", "GO_0035542__regulation_of_SNARE_complex_assembly", "GO_0035871__protein_K11-linked_deubiquitination", "GO_0036295__cellular_response_to_increased_oxygen_levels", "GO_0038061__non-canonical_NF-kappaB_signal_transduction", "GO_0038203__TORC2_signaling", "GO_0040001__establishment_of_mitotic_spindle_localization", "GO_0042255__ribosome_assembly", "GO_0042632__cholesterol_homeostasis", "GO_0043065__positive_regulation_of_apoptotic_process", "GO_0043200__response_to_amino_acid", "GO_0043276__anoikis", "GO_0044027__negative_regulation_of_gene_expression_via_chromosomal_CpG_island_methylation", "GO_0044314__protein_K27-linked_ubiquitination", "GO_0044346__fibroblast_apoptotic_process", "GO_0044571__[2Fe-2S]_cluster_assembly", "GO_0044597__daunorubicin_metabolic_process", "GO_0044598__doxorubicin_metabolic_process", "GO_0045040__protein_insertion_into_mitochondrial_outer_membrane", "GO_0045050__protein_insertion_into_ER_membrane_by_stop-transfer_membrane-anchor_sequence", "GO_0045161__neuronal_ion_channel_clustering", "GO_0045454__cell_redox_homeostasis", "GO_0045542__positive_regulation_of_cholesterol_biosynthetic_process", "GO_0045670__regulation_of_osteoclast_differentiation", "GO_0045744__negative_regulation_of_G_protein-coupled_receptor_signaling_pathway", "GO_0045792__negative_regulation_of_cell_size", "GO_0045910__negative_regulation_of_DNA_recombination", "GO_0045945__positive_regulation_of_transcription_by_RNA_polymerase_III", "GO_0046185__aldehyde_catabolic_process", "GO_0046330__positive_regulation_of_JNK_cascade", "GO_0046339__diacylglycerol_metabolic_process", "GO_0046479__glycosphingolipid_catabolic_process", "GO_0046512__sphingosine_biosynthetic_process", "GO_0046513__ceramide_biosynthetic_process", "GO_0046785__microtubule_polymerization", "GO_0046832__negative_regulation_of_RNA_export_from_nucleus", "GO_0046889__positive_regulation_of_lipid_biosynthetic_process", "GO_0048025__negative_regulation_of_mRNA_splicing__via_spliceosome", "GO_0048205__COPI_coating_of_Golgi_vesicle", "GO_0048266__behavioral_response_to_pain", "GO_0048388__endosomal_lumen_acidification", "GO_0048598__embryonic_morphogenesis", "GO_0050658__RNA_transport", "GO_0050691__regulation_of_defense_response_to_virus_by_host", "GO_0050771__negative_regulation_of_axonogenesis", "GO_0050821__protein_stabilization", "GO_0050868__negative_regulation_of_T_cell_activation", "GO_0050882__voluntary_musculoskeletal_movement", "GO_0051000__positive_regulation_of_nitric-oxide_synthase_activity", "GO_0051028__mRNA_transport", "GO_0051031__tRNA_transport", "GO_0051154__negative_regulation_of_striated_muscle_cell_differentiation", "GO_0051290__protein_heterotetramerization", "GO_0051292__nuclear_pore_complex_assembly", "GO_0051452__intracellular_pH_reduction", "GO_0051549__positive_regulation_of_keratinocyte_migration", "GO_0051895__negative_regulation_of_focal_adhesion_assembly", "GO_0060702__negative_regulation_of_endoribonuclease_activity", "GO_0060816__random_inactivation_of_X_chromosome", "GO_0060914__heart_formation", "GO_0061431__cellular_response_to_methionine", "GO_0061458__reproductive_system_development", "GO_0061668__mitochondrial_ribosome_assembly", "GO_0061795__Golgi_lumen_acidification", "GO_0061909__autophagosome-lysosome_fusion", "GO_0070131__positive_regulation_of_mitochondrial_translation", "GO_0070266__necroptotic_process", "GO_0070459__prolactin_secretion", "GO_0070682__proteasome_regulatory_particle_assembly", "GO_0070885__negative_regulation_of_calcineurin-NFAT_signaling_cascade", "GO_0070934__CRD-mediated_mRNA_stabilization", "GO_0070936__protein_K48-linked_ubiquitination", "GO_0071233__cellular_response_to_L-leucine", "GO_0071470__cellular_response_to_osmotic_stress", "GO_0071476__cellular_hypotonic_response", "GO_0071763__nuclear_membrane_organization", "GO_0071816__tail-anchored_membrane_protein_insertion_into_ER_membrane", "GO_0071919__G-quadruplex_DNA_formation", "GO_0075732__viral_penetration_into_host_nucleus", "GO_0090128__regulation_of_synapse_maturation", "GO_0090315__negative_regulation_of_protein_targeting_to_membrane", "GO_0090559__regulation_of_membrane_permeability", "GO_0097066__response_to_thyroid_hormone", "GO_0097401__synaptic_vesicle_lumen_acidification", "GO_0097700__vascular_endothelial_cell_response_to_laminar_fluid_shear_stress", "GO_0098761__cellular_response_to_interleukin-7", "GO_0099010__modification_of_postsynaptic_structure", "GO_0099173__postsynapse_organization", "GO_0106072__negative_regulation_of_adenylate_cyclase-activating_G_protein-coupled_receptor_signaling_pathway", "GO_0110095__cellular_detoxification_of_aldehyde", "GO_0110104__mRNA_alternative_polyadenylation", "GO_0140719__constitutive_heterochromatin_formation", "GO_0141005__transposable_element_silencing_by_heterochromatin_formation", "GO_0180010__co-transcriptional_mRNA_3'-end_processing__cleavage_and_polyadenylation_pathway", "GO_1900034__regulation_of_cellular_response_to_heat", "GO_1900152__negative_regulation_of_nuclear-transcribed_mRNA_catabolic_process__deadenylation-dependent_decay", "GO_1900180__regulation_of_protein_localization_to_nucleus", "GO_1901017__negative_regulation_of_potassium_ion_transmembrane_transporter_activity", "GO_1901380__negative_regulation_of_potassium_ion_transmembrane_transport", "GO_1901687__glutathione_derivative_biosynthetic_process", "GO_1901838__positive_regulation_of_transcription_of_nucleolar_large_rRNA_by_RNA_polymerase_I", "GO_1902166__negative_regulation_of_intrinsic_apoptotic_signaling_pathway_in_response_to_DNA_damage_by_p53_class_mediator", "GO_1902430__negative_regulation_of_amyloid-beta_formation", "GO_1902600__proton_transmembrane_transport", "GO_1902774__late_endosome_to_lysosome_transport", "GO_1903093__regulation_of_protein_K48-linked_deubiquitination", "GO_1903142__positive_regulation_of_establishment_of_endothelial_barrier", "GO_1903393__positive_regulation_of_adherens_junction_organization", "GO_1903608__protein_localization_to_cytoplasmic_stress_granule", "GO_1903691__positive_regulation_of_wound_healing__spreading_of_epidermal_cells", "GO_1904059__regulation_of_locomotor_rhythm", "GO_1904294__positive_regulation_of_ERAD_pathway", "GO_1904380__endoplasmic_reticulum_mannose_trimming", "GO_1904690__positive_regulation_of_cytoplasmic_translational_initiation", "GO_1905143__eukaryotic_translation_initiation_factor_2_complex_assembly", "GO_1905671__regulation_of_lysosome_organization", "GO_1905672__negative_regulation_of_lysosome_organization", "GO_1905857__positive_regulation_of_pentose-phosphate_shunt", "GO_1990166__protein_localization_to_site_of_double-strand_break", "GO_1990253__cellular_response_to_leucine_starvation", "GO_1990428__miRNA_transport", "GO_1990547__mitochondrial_phosphate_ion_transmembrane_transport", "GO_2000146__negative_regulation_of_cell_motility", "GO_2000179__positive_regulation_of_neural_precursor_cell_proliferation", "GO_2000270__negative_regulation_of_fibroblast_apoptotic_process", "GO_2000638__regulation_of_SREBP_signaling_pathway", "GO_2000660__negative_regulation_of_interleukin-1-mediated_signaling_pathway", "GO_2000738__positive_regulation_of_stem_cell_differentiation", "GO_2000767__positive_regulation_of_cytoplasmic_translation", "GO_2000785__regulation_of_autophagosome_assembly", "GO_2000975__positive_regulation_of_pro-B_cell_differentiation", "GO_0000082__G1_S_transition_of_mitotic_cell_cycle", "GO_0000338__protein_deneddylation", "GO_0000398__mRNA_splicing__via_spliceosome", "GO_0000492__box_C_D_snoRNP_assembly", "GO_0000961__negative_regulation_of_mitochondrial_RNA_catabolic_process", "GO_0001510__RNA_methylation", "GO_0001825__blastocyst_formation", "GO_0001881__receptor_recycling", "GO_0001961__positive_regulation_of_cytokine-mediated_signaling_pathway", "GO_0002398__MHC_class_Ib_protein_complex_assembly", "GO_0002502__peptide_antigen_assembly_with_MHC_class_I_protein_complex", "GO_0003084__positive_regulation_of_systemic_arterial_blood_pressure", "GO_0003091__renal_water_homeostasis", "GO_0005981__regulation_of_glycogen_catabolic_process", "GO_0006000__fructose_metabolic_process", "GO_0006098__pentose-phosphate_shunt", "GO_0006111__regulation_of_gluconeogenesis", "GO_0006167__AMP_biosynthetic_process", "GO_0006302__double-strand_break_repair", "GO_0006338__chromatin_remodeling", "GO_0006406__mRNA_export_from_nucleus", "GO_0006414__translational_elongation", "GO_0006417__regulation_of_translation", "GO_0006457__protein_folding", "GO_0006465__signal_peptide_processing", "GO_0006470__protein_dephosphorylation", "GO_0006481__C-terminal_protein_methylation", "GO_0006487__protein_N-linked_glycosylation", "GO_0006516__glycoprotein_catabolic_process", "GO_0006531__aspartate_metabolic_process", "GO_0006611__protein_export_from_nucleus", "GO_0006620__post-translational_protein_targeting_to_endoplasmic_reticulum_membrane", "GO_0006621__protein_retention_in_ER_lumen", "GO_0006754__ATP_biosynthetic_process", "GO_0006828__manganese_ion_transport", "GO_0006855__xenobiotic_transmembrane_transport", "GO_0006888__endoplasmic_reticulum_to_Golgi_vesicle-mediated_transport", "GO_0006890__retrograde_vesicle-mediated_transport__Golgi_to_endoplasmic_reticulum", "GO_0006895__Golgi_to_endosome_transport", "GO_0006900__vesicle_budding_from_membrane", "GO_0006913__nucleocytoplasmic_transport", "GO_0006974__DNA_damage_response", "GO_0006986__response_to_unfolded_protein", "GO_0006999__nuclear_pore_organization", "GO_0007005__mitochondrion_organization", "GO_0007017__microtubule-based_process", "GO_0007042__lysosomal_lumen_acidification", "GO_0007096__regulation_of_exit_from_mitosis", "GO_0007289__spermatid_nucleus_differentiation", "GO_0007612__learning", "GO_0009051__pentose-phosphate_shunt__oxidative_branch", "GO_0009794__regulation_of_mitotic_cell_cycle__embryonic", "GO_0010288__response_to_lead_ion", "GO_0010389__regulation_of_G2_M_transition_of_mitotic_cell_cycle", "GO_0010458__exit_from_mitosis", "GO_0010468__regulation_of_gene_expression", "GO_0010564__regulation_of_cell_cycle_process", "GO_0010591__regulation_of_lamellipodium_assembly", 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