Returns the registry of published module clocks: one elastic net clock per
co-expression module (plus "allmodulegenes", trained on the genes of
all modules), for the rodent and the multispecies module sets. Pass a
returned (filtered) data frame to download_clocks, which
fetches the archive each set is published as.
Value
A data frame with columns filename, type,
outcome, species, tissue, scaling,
color, function (the module's annotated biological process)
and archive (the Zenodo archive holding the file).
Examples
list_module_clocks(outcome = "Mortality", species = "Rodents")
#> filename
#> 1 EN_Moduleclock_Mortality_Rodents_Multitissue_allmodulegenes_scaleddiff.pkl
#> 2 EN_Moduleclock_Mortality_Rodents_Multitissue_black_scaleddiff.pkl
#> 3 EN_Moduleclock_Mortality_Rodents_Multitissue_blue_scaleddiff.pkl
#> 4 EN_Moduleclock_Mortality_Rodents_Multitissue_brown_scaleddiff.pkl
#> 5 EN_Moduleclock_Mortality_Rodents_Multitissue_cyan_scaleddiff.pkl
#> 6 EN_Moduleclock_Mortality_Rodents_Multitissue_darkgreen_scaleddiff.pkl
#> 7 EN_Moduleclock_Mortality_Rodents_Multitissue_darkgrey_scaleddiff.pkl
#> 8 EN_Moduleclock_Mortality_Rodents_Multitissue_darkorange_scaleddiff.pkl
#> 9 EN_Moduleclock_Mortality_Rodents_Multitissue_darkred_scaleddiff.pkl
#> 10 EN_Moduleclock_Mortality_Rodents_Multitissue_green_scaleddiff.pkl
#> 11 EN_Moduleclock_Mortality_Rodents_Multitissue_greenyellow_scaleddiff.pkl
#> 12 EN_Moduleclock_Mortality_Rodents_Multitissue_grey60_scaleddiff.pkl
#> 13 EN_Moduleclock_Mortality_Rodents_Multitissue_lightgreen_scaleddiff.pkl
#> 14 EN_Moduleclock_Mortality_Rodents_Multitissue_lightyellow_scaleddiff.pkl
#> 15 EN_Moduleclock_Mortality_Rodents_Multitissue_magenta_scaleddiff.pkl
#> 16 EN_Moduleclock_Mortality_Rodents_Multitissue_midnightblue_scaleddiff.pkl
#> 17 EN_Moduleclock_Mortality_Rodents_Multitissue_orange_scaleddiff.pkl
#> 18 EN_Moduleclock_Mortality_Rodents_Multitissue_pink_scaleddiff.pkl
#> 19 EN_Moduleclock_Mortality_Rodents_Multitissue_red_scaleddiff.pkl
#> 20 EN_Moduleclock_Mortality_Rodents_Multitissue_salmon_scaleddiff.pkl
#> 21 EN_Moduleclock_Mortality_Rodents_Multitissue_skyblue_scaleddiff.pkl
#> 22 EN_Moduleclock_Mortality_Rodents_Multitissue_tan_scaleddiff.pkl
#> 23 EN_Moduleclock_Mortality_Rodents_Multitissue_turquoise_scaleddiff.pkl
#> 24 EN_Moduleclock_Mortality_Rodents_Multitissue_yellow_scaleddiff.pkl
#> type outcome species tissue scaling color
#> 1 EN Mortality Rodents Multi-Tissue Scaled allmodulegenes
#> 2 EN Mortality Rodents Multi-Tissue Scaled black
#> 3 EN Mortality Rodents Multi-Tissue Scaled blue
#> 4 EN Mortality Rodents Multi-Tissue Scaled brown
#> 5 EN Mortality Rodents Multi-Tissue Scaled cyan
#> 6 EN Mortality Rodents Multi-Tissue Scaled darkgreen
#> 7 EN Mortality Rodents Multi-Tissue Scaled darkgrey
#> 8 EN Mortality Rodents Multi-Tissue Scaled darkorange
#> 9 EN Mortality Rodents Multi-Tissue Scaled darkred
#> 10 EN Mortality Rodents Multi-Tissue Scaled green
#> 11 EN Mortality Rodents Multi-Tissue Scaled greenyellow
#> 12 EN Mortality Rodents Multi-Tissue Scaled grey60
#> 13 EN Mortality Rodents Multi-Tissue Scaled lightgreen
#> 14 EN Mortality Rodents Multi-Tissue Scaled lightyellow
#> 15 EN Mortality Rodents Multi-Tissue Scaled magenta
#> 16 EN Mortality Rodents Multi-Tissue Scaled midnightblue
#> 17 EN Mortality Rodents Multi-Tissue Scaled orange
#> 18 EN Mortality Rodents Multi-Tissue Scaled pink
#> 19 EN Mortality Rodents Multi-Tissue Scaled red
#> 20 EN Mortality Rodents Multi-Tissue Scaled salmon
#> 21 EN Mortality Rodents Multi-Tissue Scaled skyblue
#> 22 EN Mortality Rodents Multi-Tissue Scaled tan
#> 23 EN Mortality Rodents Multi-Tissue Scaled turquoise
#> 24 EN Mortality Rodents Multi-Tissue Scaled yellow
#> function archive
#> 1 All Modules Rodent module clocks
#> 2 Myogenesis/Muscle contraction Rodent module clocks
#> 3 Respiration/Mitochondrial translation Rodent module clocks
#> 4 Chromatin modification/Transcription Rodent module clocks
#> 5 Heme metabolism Rodent module clocks
#> 6 Cell adhesion/VEGF signaling Rodent module clocks
#> 7 Protein processing/mTOR signaling Rodent module clocks
#> 8 Lipid met/PPAR signaling Rodent module clocks
#> 9 Cholesterol met/mTOR signaling Rodent module clocks
#> 10 Cell cycle Rodent module clocks
#> 11 ECM organization/EMT Rodent module clocks
#> 12 Apoptosis/Nrf2 signaling/Proteasome Rodent module clocks
#> 13 Interferon signaling Rodent module clocks
#> 14 Nrf2 signaling/Proteasome Rodent module clocks
#> 15 Amino acid met/Coagulation/Xenobiotic met Rodent module clocks
#> 16 mRNA splicing Rodent module clocks
#> 17 Fatty acid met/Peroxisome Rodent module clocks
#> 18 Adaptive immunity/T cell signaling Rodent module clocks
#> 19 Translation/Ribosome Rodent module clocks
#> 20 Cholesterol met/Platelet degranulation Rodent module clocks
#> 21 Heat stress response Rodent module clocks
#> 22 Oxidative phosphorylation/TCA cycle Rodent module clocks
#> 23 Innate immunity/Inflammation Rodent module clocks
#> 24 Chromatin modification/Transcription 2 Rodent module clocks