lasseignelab · lizzyjoan · May 1, 2026 · Nov 24, 2025 · Nov 24, 2025 · Nov 24, 2025
diff --git a/.gitignore b/.gitignore
@@ -241,6 +241,9 @@ bin/conda/work/
 bin/conda/work/*
 bin/conda/.nextflow/
 bin/container/*
+bin/docker/
+src/lint_and_style.sh
+src/lint_and_style.sh
 Rplots.pdf
 src/lint_and_style.sh
 megalinter-reports
diff --git a/data/241203_setbp1_targets_names_only.csv b/data/241203_setbp1_targets_names_only.csv
@@ -0,0 +1,251 @@
+
+RPS6KL1
+MT-TF
+MT-RNR1
+PTGER2
+PPP2R4 (PTPA)
+PTGS2
+HOXA10
+HOXA9
+RAD52
+TTC23
+ZEB1
+PBRM1
+RALGAPA1
+CZIB (C1orf123)
+EMC8
+NDUFAB1
+PAF1
+MKS1
+PPP5C
+BRCA1
+TBC1D23
+CLEC16A
+RIOK2
+MPC1
+EIF4B
+MED29
+PKN2
+ZC3H15
+MYO9A
+EED
+ZZEF1
+TUBE1
+MEF2C
+MECOM
+CHERP
+TGDS
+CRLS1
+USP48
+PDPR
+WDR7
+TXNL1
+MZF1
+PSMD8
+EIF3D
+HM13
+CEP192
+MCTS2P
+TAZ
+NDFIP2
+PHKB
+NARFL
+MAP4K1
+SARS2
+RPS16
+ZNF862
+FKTN
+ZNF330
+GGCX
+KIAA2013
+ZNHIT6
+DPH5
+DIEXF
+CASC1
+VAMP8
+FKBP15
+CDKN2C
+NCOA5
+C16orf70
+RAP2A
+PCNX4
+DGCR6L
+MRPS12
+MBD4
+ITFG1
+TTI2
+NSUN5
+LSM 4.00
+COX4I1
+DCAF8
+CDK8
+IPO8
+LRRCC1
+ELP3
+CEPT1
+ZC3H10
+EPC2
+EPRS
+SLC31A1
+MRPL15
+TMTC3
+ESYT1
+NAA30
+LINS1
+PSMB6
+PIGK
+HAX1
+TMEM177
+ZMAT2
+GOLGA7
+TAF5
+CHEK1
+DLAT
+CACUL1
+CWF19L2
+HS2ST1
+TSEN2
+CCDC174
+DRAM2
+UTP14A
+FBRS
+AASDH
+RNF111
+CNOT11
+UBR1
+C1orf123
+KLHDC9
+DPY30
+C4orf36
+IFT122
+GNL3
+PDSS2
+NOL6
+ARL5B
+BAG5
+SENP8
+LEO1
+CYB5D2
+E4F1
+NDUFS5
+NUDT9
+AC093323.3
+RNF139
+ETFDH
+AFF1
+CNIH2
+NAALADL2
+CCDC184
+BET1L
+RIC8A
+EIF3K
+MRFAP1L1
+MRFAP1
+TRAPPC5
+MRPS16
+SEP15
+ASB7
+RBM33
+FAF1
+FAM174B
+FAAP100
+TCEA1
+AC007731.1
+NBR1
+SUPT5H
+ANAPC7
+TOMM7
+DDI2
+TAF13
+NBR2
+MT-ND6
+CEP290
+MTCO3P12
+MT-ND1
+KIF1BP
+FAM229B
+TIMM23B
+TBC1D8
+C4orf46
+LYRM5
+KLRC2
+DNAJC19
+MT-TL1
+MT-TE
+MT-TT
+MT-TP
+CENPBD1P1
+RP11-252A24.2
+NEURL4
+AC009403.2
+AC026954.6
+SUGT1P
+PARG
+DNAJC9-AS1
+RP11-235C23.5
+RP5-857K21.4
+MCTS1
+NDFIP2-AS1
+RP11-421L21.3
+DNAJC9-AS1
+ZEB1-AS1
+SNORD13
+PARGP1
+NSUN6
+SOX2-OT
+RNF139-AS1
+RNF139
+MTND5P11
+RP11-680H20.2
+RP11-539L10.3
+EEF1G
+RP11-277P12.6
+APOPT1
+RP11-73M18.2
+RP11-16B13.1
+RP5-1024G6.7
+RP1-168L15.5
+MIR4461
+TIMM23
+RP11-773H22.4
+RP11-242D8.1
+RP11-242D8.3
+CTD-3222D19.12
+RP11-646I6.5
+RP5-1103G7.10
+XXbac-B444P24.14
+MCM8-AS1
+RP5-912I13.2
+RP11-472I20.4
+SET
+Set
+Hoxa10
+Hoxa9
+CTNNBL1
+ABT1
+SFR1
+PTPA
+CDKN2A
+PTPRA
+O35381/Q9Z180
+Q8IY57
+Q9BXN6
+Q9NY87
+Q9P1C9
+Q9H8W4
+Q9HD64
+Q9NS26
+G2XKQ0
+342666
+Q7KZS0
+P06821
+P0DOF5
+Q9NS26
+Q7KZS0
+Q9H8W4
+Q9BXN6
+P0DOF2
+Q93079
+CHEBI:6092
+P51957-1
+Q15326
diff --git a/data/241203_setbp1_targets_prioritized.csv b/data/241203_setbp1_targets_prioritized.csv
@@ -0,0 +1,31 @@
+target,pan-go,pan-go class,pharos
+EIF4B,formation of translation preinitiation complex,Translation,Tbio
+MCTS1,formation of translation preinitiation complex,Translation,Tbio
+MCTS2P,formation of translation preinitiation complex,Translation,Tbio
+RPS16,translation/peptide biosynthesis,Translation,Tbio
+EIF3D,translation/peptide biosynthesis,Translation,Tbio
+EPRS,translation/peptide biosynthesis,Translation,Tchem
+PAF1,gene expression/Pol II elongation,Pol II/Elongation,Tbio
+TAF5,gene expression/initiation,Pol II/Elongation,Tbio
+TAF13,gene expression/initiation,Pol II/Elongation,Tbio
+SUPT5H,RNA metabolic process/elongation,Pol II/Elongation,Tbio
+ABT1,gene expression/basal transcription,Pol II/Elongation,Tbio
+EED,chromatin regulation,Chromatin,Tchem
+TIMM23,mitochondrial protein import (TIM23),Mito Import,Tbio
+TIMM23B,mitochondrial protein import (TIM23),Mito Import,Tdark
+DNAJC19,mitochondrial import/cardiolipin remodeling,Mito Import,Tbio
+DLAT,pyruvate dehydrogenase (PDC),PDH/Metabolism,Tbio
+PDPR,pyruvate dehydrogenase phosphatase (PDP),PDH/Metabolism,Tbio
+MRPL15,mitochondrial translation,Mito Ribosome,Tdark
+MRPS16,mitochondrial translation,Mito Ribosome,Tbio
+COX4I1,OXPHOS complex IV,OXPHOS,Tbio
+ETFDH,electron transfer flavoprotein dehydrogenase,OXPHOS,Tbio
+MPC1,mitochondrial pyruvate carrier,Pyruvate Import,Tbio
+PTGER2,cellular response to prostaglandin E stimulus,Prostaglandin,
+PTGS2,prostaglandin biosynthetic process/COX-2,Prostaglandin,Tclin
+MAP4K1,MAPK cascade,Kinase,Tchem
+PKN2,Rho/PKN signaling,Kinase,Tchem
+MEF2C,neurodevelopment/synaptic programs,Neuro TF,Tbio
+NSUN5,RNA metabolic process (rRNA methyltransferase),RNA Mod,Tbio
+NSUN6,RNA metabolic process (tRNA methyltransferase),RNA Mod,Tbio
+ELP3,RNA metabolic process (tRNA wobble/acetyltransferase),RNA Mod,Tbio
diff --git a/results/figures/approved_drugs_braincells_full.png b/results/figures/approved_drugs_braincells_full.png
diff --git a/results/figures/approved_drugs_braincells_multiplecells.png b/results/figures/approved_drugs_braincells_multiplecells.png
diff --git a/results/figures/approved_drugs_braincells_topWTCS.png b/results/figures/approved_drugs_braincells_topWTCS.png
diff --git a/results/figures/approved_drugs_top_moa.png b/results/figures/approved_drugs_top_moa.png
diff --git a/results/figures/drug_targets_histogram.png b/results/figures/drug_targets_histogram.png
diff --git a/results/figures/figure_5.png b/results/figures/figure_5.png
diff --git a/results/figures/full_drug_safety_anno_table.csv b/results/figures/full_drug_safety_anno_table.csv
diff --git a/results/figures/setbp1_drug_shared_targets_trialphase.png b/results/figures/setbp1_drug_shared_targets_trialphase.png
diff --git a/results/figures/setbp1_drugs_shared.png b/results/figures/setbp1_drugs_shared.png
diff --git a/results/figures/setbp1_drugs_shared_phase.png b/results/figures/setbp1_drugs_shared_phase.png
diff --git a/results/figures/setbp1_drugs_shared_targets.png b/results/figures/setbp1_drugs_shared_targets.png
diff --git a/results/signature_reversion/approved_drugs_res.csv b/results/signature_reversion/approved_drugs_res.csv
diff --git a/results/signature_reversion/approveddrugs_target_exp_heatmap.png b/results/signature_reversion/approveddrugs_target_exp_heatmap.png
diff --git a/results/signature_reversion/brain_drugs_filtered.csv b/results/signature_reversion/brain_drugs_filtered.csv
diff --git a/results/signature_reversion/drug_safety_data.csv b/results/signature_reversion/drug_safety_data.csv