Skip to content

Commit

Permalink
Merge pull request #83 from loucerac/develop
Browse files Browse the repository at this point in the history 
Develop
  • Loading branch information
@loucerac
loucerac authored Feb 27, 2024
2 parents c657392 + 3c29386 commit 0c7b05d
Show file tree
Hide file tree
Showing 46 changed files with 849,926 additions and 6 deletions.
3 changes: 2 additions & 1 deletion .gitignore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -294,4 +294,5 @@ dask-worker-space/
examples/fanconi_anemia/results/tmp/
examples/codeocean/results/tmp/
debug/
.debug/
.debug/
examples/benchmark/experiments/
224 changes: 224 additions & 0 deletions NES_FMdrug_targets.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,224 @@
drug_id pval NES target drug
DB00188 7.99474856557809e-15 2.90901159697069 PSMB1 Bortezomib
DB08889 7.99474856557809e-15 2.90901159697069 PSMB1 Carfilzomib
DB09570 7.99474856557809e-15 2.90901159697069 PSMD1 NA
DB11991 7.99474856557809e-15 2.90901159697069 PSMD1 NA
DB01238 8.70726813404579e-14 2.84686264847439 DRD1 Aripiprazole
DB05016 6.687515432598e-16 2.83183992665024 RPSA NA
DB00334 2.3751753526728e-10 2.66958934149934 DRD1 Olanzapine
DB00201 4.5116149763741e-11 2.65389821728204 ADORA1 Caffeine
DB12010 1.06154629634606e-23 2.62933940421315 ABL1 Fostamatinib
DB00945 6.86152566631974e-10 2.59745745472547 PTGS1 Acetylsalicylic acid
DB00543 7.68674738167459e-10 2.59523917219978 DRD1 Amoxapine
DB00408 1.42735198322292e-09 2.58588102299172 DRD1 Loxapine
DB01017 2.17497469078413e-09 2.57617939619727 NOS2 Minocycline
DB01224 2.32255224737196e-09 2.57060661923346 DRD1 Quetiapine
DB00363 1.08421302204266e-08 2.54111613055279 DRD1 Clozapine
DB14185 5.96573299463495e-09 2.53328898266315 DRD1 Aripiprazole lauroxil
DB12745 4.1078017787792e-09 2.52498371750248 PRKD3 NA
DB00806 1.81052765150084e-08 2.52334855092222 ADORA1 Pentoxifylline
DB11762 2.12933236326908e-08 2.50639900645563 PSMB2 NA
DB00631 3.51583890422403e-09 2.48875750395447 RRM1 Clofarabine
DB00477 2.1010476350104e-08 2.47906930513521 DRD1 Chlorpromazine
DB06216 1.22618367888845e-07 2.4385075342421 DRD1 Asenapine
DB00248 1.29884512369048e-07 2.43426838589647 DRD1 Cabergoline
DB09283 1.08499507267747e-07 2.41916036037185 PDGFRB Trapidil
DB04961 5.3225087715393e-09 2.41474994595508 POLA1 NA
DB03496 7.75436615706588e-09 2.40590505563644 EGFR Alvocidib
DB11638 3.24328331363999e-09 2.40435833344604 LDHB Artenimol
DB01169 3.46474644005674e-10 2.39297121375542 AKT1 Arsenic trioxide
DB00726 3.0597147065842e-07 2.38673964775741 ADRA2A Trimipramine
DB08901 8.5953847077601e-07 2.36880500737295 ABL1 Ponatinib
DB08142 1.19788295387709e-06 2.36508212317729 CDK2 AT-7519
DB12686 1.19788295387709e-06 2.36508212317729 CDK1 NA
DB00696 9.47694216007032e-07 2.36338376852002 ADRA2A Ergotamine
DB06148 1.80991162802631e-06 2.35879756384779 HRH4 Mianserin
DB08515 3.04758465441819e-07 2.35446468113583 PSMB1 (3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE
DB00320 1.58045989951353e-06 2.35366778752393 HTR4 Dihydroergotamine
DB01403 1.78724337358134e-06 2.34611468802194 DRD1 Methotrimeprazine
DB01142 2.05310862795753e-06 2.33957859394792 CHRM3 Doxepin
DB00987 5.28323794537887e-07 2.33190454510424 POLB Cytarabine
DB01200 1.05757189577476e-06 2.32795232993289 DRD1 Bromocriptine
DB00715 1.04043607910131e-06 2.32170411234523 HTR2B Paroxetine
DB00458 1.47003676010841e-06 2.31189332757827 CHRM3 Imipramine
DB06153 5.49018102437954e-06 2.29594817197345 CHRM3 Pizotifen
DB00934 2.16902502770736e-06 2.28395195585229 CHRM3 Maprotiline
DB11651 1.07391716710688e-07 2.28001702767195 MTOR NA
DB11896 1.07391716710688e-07 2.28001702767195 MTOR NA
DB11974 1.07391716710688e-07 2.28001702767195 MTOR NA
DB12180 1.07391716710688e-07 2.28001702767195 MTOR NA
DB12400 1.07391716710688e-07 2.28001702767195 MTOR NA
DB12703 1.07391716710688e-07 2.28001702767195 MTOR NA
DB01151 5.70789601012772e-06 2.2737406828557 CHRM3 Desipramine
DB10772 2.98183878661962e-06 2.2735326382889 VEGFA Foreskin keratinocyte (neonatal)
DB02746 1.50347475431237e-07 2.27176999434507 PPARA Phthalic Acid
DB01186 4.18153713231524e-06 2.2571944814816 DRD1 Pergolide
DB00421 3.38663829413554e-06 2.25551336485983 AR Spironolactone
DB11891 5.68786610977567e-06 2.25011172750546 PIK3CD NA
DB09194 5.985657493724e-06 2.24583393620288 HTR2A Etoperidone
DB11663 3.16133440797789e-08 2.24456330961327 PIK3R1 NA
DB11666 3.16133440797789e-08 2.24456330961327 PIK3R1 NA
DB11772 3.16133440797789e-08 2.24456330961327 PIK3CA Pilaralisib
DB11962 3.16133440797789e-08 2.24456330961327 PIK3R1 NA
DB12108 3.16133440797789e-08 2.24456330961327 PIK3R1 NA
DB12601 3.16133440797789e-08 2.24456330961327 PIK3R1 NA
DB13051 3.16133440797789e-08 2.24456330961327 PIK3R1 NA
DB14980 3.16133440797789e-08 2.24456330961327 PIK3R1 NA
DB15186 3.16133440797789e-08 2.24456330961327 PIK3R1 NA
DB00975 5.28316227100425e-06 2.24401598576015 PDE5A Dipyridamole
DB05294 5.71804596343451e-06 2.24346426661368 VEGFA Vandetanib
DB06595 1.35420916782337e-05 2.22771350701768 FLT3 Midostaurin
DB06195 1.14462087755243e-07 2.22099060665705 MAPK1 Seliciclib
DB01221 1.09853061689679e-05 2.2158449129261 NOS1 Ketamine
DB00852 1.99514524485434e-05 2.20869768160017 ADRB1 Pseudoephedrine
DB12174 8.63072126679029e-06 2.20387318478638 EGFR NA
DB00568 2.43276092842468e-05 2.19883479321762 CACNA1I Cinnarizine
DB00734 2.17520213768915e-05 2.19706054921895 DRD1 Risperidone
DB08896 2.05903761137068e-05 2.18540421461993 ABL1 Regorafenib
DB00540 3.86592518209711e-05 2.18346881406462 HTR1A Nortriptyline
DB02010 1.8074503164692e-05 2.16878201316931 CHRM1 Staurosporine
DB00675 2.76900980721005e-05 2.16432970261789 KCNH2 Tamoxifen
DB05608 3.08588077908472e-05 2.1612088297363 KDR NA
DB00589 8.66852912910948e-05 2.16117001296366 DRD1 Lisuride
DB01049 1.67106953204435e-05 2.15502877009903 HTR1A Ergoloid mesylate
DB13345 1.67106953204435e-05 2.15502877009903 HTR1A Dihydroergocristine
DB00321 2.06560176125201e-05 2.14842194494534 HRH2 Amitriptyline
DB00153 4.38321074228977e-05 2.1366793896395 VDR Ergocalciferol
DB01267 0.000135293831085707 2.13540337203546 DRD1 Paliperidone
DB09167 9.63374602636345e-05 2.12403949599069 CHRM3 Dosulepin
DB12695 2.28775913064995e-05 2.12389689688192 TUBB1 Phenethyl Isothiocyanate
DB05075 4.98464866459611e-05 2.1198619268814 FLT4 TG-100801
DB00502 0.000205482349895687 2.11584156578195 DRD1 Haloperidol
DB00230 6.86796854382199e-05 2.10109254227129 CACNA2D1 Pregabalin
DB08872 6.86796854382199e-05 2.10109254227129 CACNA2D1 Gabapentin enacarbil
DB12032 6.86796854382199e-05 2.10109254227129 CACNA1H NA
DB12105 6.86796854382199e-05 2.10109254227129 CACNA1H NA
DB01254 7.31352879427239e-05 2.09787102063637 ABL1 Dasatinib
DB05492 0.000158647052714554 2.09662583217593 ADRA2A Epicept NP-1
DB00131 0.00013135522542339 2.09607240631919 PRKAB1 Adenosine phosphate
DB15822 9.63961361468173e-05 2.09601277486308 FLT3 Pralsetinib
DB12147 3.20102558427445e-05 2.08920028855219 PDGFRB Erdafitinib
DB10770 0.000112273315737335 2.08858910240704 FLT1 Foreskin fibroblast (neonatal)
DB00777 3.25065290148002e-05 2.08723107701789 HRH1 Propiomazine
DB11752 2.54421859000835e-05 2.08375750602786 PTGS2 Bryostatin 1
DB08804 0.000214581089437796 2.0824685412451 AR Nandrolone decanoate
DB09079 0.000214581089437796 2.08241461946912 FLT4 Nintedanib
DB02709 9.41673922991036e-05 2.08098776950237 PTGS1 Resveratrol
DB00668 3.64767191849374e-05 2.0800345955419 ADRB1 Epinephrine
DB05015 0.000155989377806822 2.06763305062866 HDAC1 Belinostat
DB06603 0.000155989377806822 2.06763305062866 HDAC1 Panobinostat
DB11841 0.000155989377806822 2.06763305062866 HDAC1 NA
DB12291 0.000155989377806822 2.06763305062866 HDAC1 NA
DB12565 0.000155989377806822 2.06763305062866 HDAC1 Abexinostat
DB00246 7.03368838024421e-05 2.06659258539973 DRD1 Ziprasidone
DB01223 0.000161950676173827 2.06330993708752 ADORA1 Aminophylline
DB01303 0.000161950676173827 2.06330993708752 ADORA1 Oxtriphylline
DB00714 0.000237530990593878 2.06081994177782 DRD1 Apomorphine
DB04946 0.000177847484542044 2.05740822389784 DRD1 Iloperidone
DB00622 0.000515078725666598 2.05596540628483 CHRM3 Nicardipine
DB01708 8.54425849882157e-05 2.04705511628778 PPARA Prasterone
DB12369 0.000237636876256669 2.04425698625076 PRKD3 NA
DB00619 0.000101458677007772 2.04124880343158 ABL1 Imatinib
DB00434 0.000123557929362233 2.03097159123595 CHRM3 Cyproheptadine
DB04216 0.000193251988943567 2.02908132166263 ESR1 Quercetin
DB06229 0.000341476127838962 2.02592408731814 ADRA2A Ocaperidone
DB00193 0.000419268444895394 2.02315944022508 ADORA1 Tramadol
DB12267 0.00016574763062438 2.02033578221135 ABL1 Brigatinib
DB00996 0.000265242461471292 2.01627560553729 ADORA1 Gabapentin
DB15442 5.91720169969787e-06 2.01603641449277 CDK5 Trilaciclib
DB00315 0.000108881652364272 2.01601858798298 HTR1A Zolmitriptan
DB01365 0.000216033027008778 2.00795210246365 ADRB1 Mephentermine
DB11124 0.000216033027008778 2.00795210246365 ADRB1 Racepinephrine
DB11278 0.000216033027008778 2.00795210246365 ADRB1 DL-Methylephedrine
DB11694 0.000291285378858784 2.00751731547758 PDGFRB NA
DB06738 0.000139332452909161 2.00696066375453 OPRD1 Ketobemidone
DB00182 0.000295195191404227 2.00598851726276 SLC18A2 Amphetamine
DB00228 5.13018585584395e-05 2.00567177901222 GLRA1 Enflurane
DB01393 5.96232598793836e-05 2.00171226062928 PPARA Bezafibrate
DB00368 0.000753727478011569 1.99566678564263 SLC18A2 Norepinephrine
DB00210 0.000272563559005937 1.99518251360128 RXRB Adapalene
DB11653 1.04035519409225e-08 1.99446764719816 MC2R Bremelanotide
DB11273 0.000310885002819474 1.99040256065625 HTR1A Dihydroergocornine
DB01041 0.000184181237982994 1.98814118630678 PTGS2 Thalidomide
DB03756 3.02491093387499e-05 1.98009546680489 PPARA Doconexent
DB01645 0.00065646272251272 1.97812131571348 ESR1 Genistein
DB00935 0.000381587273513955 1.97748989033185 ADRA2A Oxymetazoline
DB00454 0.000758590705327345 1.97488407698403 GRIN1 Meperidine
DB11800 0.000638162198473261 1.97465466847788 FLT4 Tivozanib
DB06616 0.000259894519577172 1.9684709221473 ABL1 Bosutinib
DB06262 0.000259894519577172 1.96752526791003 ADRB1 Droxidopa
DB01239 0.000407508144549749 1.96734259767023 DRD1 Chlorprothixene
DB00396 0.00026795310538722 1.96448213900423 ESR1 Progesterone
DB11823 0.00026795310538722 1.9638105370503 GRIN2B Esketamine
DB00242 0.000555934723024966 1.95928883163884 PNP Cladribine
DB02482 0.000555934723024966 1.95830176812855 MAPK1 Phosphonothreonine
DB02733 2.39042957227525e-06 1.95126543412538 MAPK1 Purvalanol
DB00412 0.000220268968714833 1.95025042194563 PPARA Rosiglitazone
DB16656 8.0210723460485e-05 1.94649485989667 JAK2 NA
DB04395 0.000680675949113651 1.94285380071189 GSS Phosphoaminophosphonic Acid-Adenylate Ester
DB00247 0.000604260128496866 1.93993313937696 HTR1A Methysergide
DB01183 0.000282025022472789 1.93901089717342 ESR1 Naloxone
DB00659 0.000807521847644423 1.93777189281593 GABBR1 Acamprosate
DB00370 0.000360627093627063 1.93648251794859 ADRA2A Mirtazapine
DB09078 0.000368685716712275 1.93473501858805 FLT4 Lenvatinib
DB00398 0.000384802968034252 1.9288138134451 FLT4 Sorafenib
DB06144 0.000818009144367078 1.92419880741975 KCNH2 Sertindole
DB08862 0.000185857441459359 1.91790926894491 RAF1 Cholecystokinin
DB00342 0.00059165988046264 1.8984958655982 CHRM3 Terfenadine
DB11967 0.000286871260659341 1.89751487072201 TNF Binimetinib
DB00459 0.000748881890654581 1.88465085805828 RXRB Acitretin
DB05157 5.03867423614668e-08 1.87055027054322 MAPK14 KC706
DB05210 0.000168012058227957 1.86371886416379 PIK3R1 SF1126
DB05241 0.000168012058227957 1.86371886416379 PIK3CG XL765
DB13751 0.000618055320774502 1.85558183141097 LPL Glycyrrhizic acid
DB00940 0.000659534940467998 1.85237972711397 CHRM3 Methantheline
DB09130 3.80133473108624e-05 1.84621289915531 IDH3A Copper
DB01614 0.000775678041623119 1.84184819360542 DRD1 Acepromazine
DB08059 4.9483452532993e-05 1.81232017116223 PIK3R1 Wortmannin
DB00571 0.000687132931972087 1.80994568361129 ADRB1 Propranolol
DB00960 0.000687132931972087 1.80994568361129 ADRB1 Pindolol
DB08807 0.000687132931972087 1.80994568361129 ADRB1 Bopindolol
DB01428 7.63021777103283e-05 1.80645315863015 ESR1 Oxybenzone
DB11219 7.63021777103283e-05 1.80645315863015 ESR1 Enzacamene
DB07859 7.94594601426685e-05 1.80552486575556 GSK3B 4-(4-CHLOROPHENYL)-4-[4-(1H-PYRAZOL-4-YL)PHENYL]PIPERIDINE
DB07947 7.94594601426685e-05 1.80552486575556 GSK3B ISOQUINOLINE-5-SULFONIC ACID (2-(2-(4-CHLOROBENZYLOXY)ETHYLAMINO)ETHYL)AMIDE
DB08073 7.94594601426685e-05 1.80552486575556 GSK3B (2S)-1-(1H-INDOL-3-YL)-3-{[5-(3-METHYL-1H-INDAZOL-5-YL)PYRIDIN-3-YL]OXY}PROPAN-2-AMINE
DB02116 8.57740303145613e-05 1.80381300299071 CDK5 Olomoucine
DB04224 9.31410361752856e-05 1.80131952266457 PPARA Oleic Acid
DB07724 9.31410361752856e-05 1.80131952266457 PPARA Indeglitazar
DB01185 0.000278470793642167 1.76907787885827 ESR1 Fluoxymesterone
DB05969 0.00028272217418809 1.76890427842478 VEGFA SNS-032
DB12021 0.00028272217418809 1.76890427842478 CDK9 NA
DB06521 0.000367749982537227 1.75658355210739 PPARA Ertiprotafib
DB01622 0.000722042404054918 1.73692906012489 DRD1 Thioproperazine
DB02587 0.000730587185437611 1.73610380358445 CFTR Colforsin
DB01196 0.000824579848047984 1.73286649744415 ESR1 Estramustine
DB09073 1.29336104252088e-08 1.72244828127743 CDK6 Palbociclib
DB12681 8.24066929049248e-06 1.71129931400409 HRAS NA
DB09121 2.84955202699251e-05 1.70431441884489 ADCY1 Aurothioglucose
DB06843 3.06259665938564e-05 1.70350846940344 GNAS 2',5'-DIDEOXY-ADENOSINE 3'-MONOPHOSPHATE
DB00040 8.18936710144307e-05 1.69638924933733 GCGR Glucagon
DB09086 0.000330817892314866 1.67624051330118 ESR1 Eugenol
DB06927 0.000330817892314866 1.67610618839427 ESR1 [5-HYDROXY-2-(4-HYDROXYPHENYL)-1-BENZOFURAN-7-YL]ACETONITRILE
DB11648 0.000374061481093358 1.6747629393252 AKT2 NA
DB11743 0.000374061481093358 1.6747629393252 AKT2 NA
DB11969 0.000374061481093358 1.6747629393252 AKT2 NA
DB12218 0.000374061481093358 1.6747629393252 AKT2 NA
DB14636 0.000374061481093358 1.6747629393252 AKT2 NA
DB08094 0.000374061481093358 1.67462861441829 CDK2 RO-4584820
DB06641 0.000378385843393855 1.67409131479066 AKT1 Perifosine
DB11798 0.000534531974173999 1.66589749546929 MAPK9 NA
DB12432 0.000534531974173999 1.66589749546929 MAPK9 NA
DB15624 0.000534531974173999 1.66589749546929 MAPK10 Halicin
DB00957 0.000864806006172975 1.65434555347522 ESR1 Norgestimate
DB11064 0.000864806006172975 1.65434555347522 ESR1 Homosalate
DB11730 1.50170175025544e-05 1.53396186253186 CDK6 Ribociclib
DB12001 1.50170175025544e-05 1.53396186253186 CDK6 Abemaciclib
DB04338 5.73838058690597e-05 1.53240672689957 MAPK1 SB220025
DB08521 5.73838058690597e-05 1.53240672689957 MAPK1 4-[4-(4-Fluorophenyl)-2-[4-[(R)-methylsulfinyl]phenyl]-1H-imidazol-5-yl]pyridine
DB13930 6.28487722059388e-05 1.5322871010817 MAPK1 Ulixertinib
DB15281 6.28487722059388e-05 1.5322871010817 MAPK1 NA
DB12270 0.000395173146988534 1.52582730691678 MAPK11 NA
DB12325 0.000483653183612013 1.5246310487381 TP53 NA
DB15299 0.000483653183612013 1.5246310487381 TP53 NA
DB01285 0.000625639577796671 1.52235815819859 MC2R Corticotropin
13 changes: 13 additions & 0 deletions drexml.Rproj
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
Version: 1.0

RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default

EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8

RnwWeave: Sweave
LaTeX: pdfLaTeX
8 changes: 4 additions & 4 deletions drexml/plotting.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -240,7 +240,7 @@ def plot_gene_profile(self, gene: str, output_folder=None):
else: # pragma: no cover
plt.show()

def plot_metrics(self, width=2.735, output_folder=None):
def plot_metrics(self, width=3.3, output_folder=None):
"""
Read the drexml results TSV file and plot it. The R^2 confidence interval for the
mean go to y-axis, whereas the x-axis shows the 95% interval for the Nogueiras's
Expand Down Expand Up @@ -296,9 +296,9 @@ def plot_metrics(self, width=2.735, output_folder=None):
label="Stability 95% CI",
)

ax.axvspan(0, 0.4, color="red", alpha=0.1)
ax.axvspan(0.4, 0.75, color="y", alpha=0.1)
ax.axvspan(0.75, 1.0, color="g", alpha=0.1)
ax.axvspan(0, 0.4, color="red", alpha=0.1, label="Stab. Low")
ax.axvspan(0.4, 0.75, color="y", alpha=0.1, label="Stab. Medium")
ax.axvspan(0.75, 1.0, color="g", alpha=0.1, label="Stab. High")
ax.set_xticks([0, 0.4, 0.75, 1])

plt.xlabel("Stability")
Expand Down
2 changes: 2 additions & 0 deletions examples/.gitignore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,3 +2,5 @@
!*.pdf
*.tsv
tmp/
*.gct
*.xz
Binary file added examples/DTSEA_comparison/C0015625_disease_gda_summary.zip
View file
Binary file not shown.
Loading

0 comments on commit 0c7b05d

Please sign in to comment.