├── AUCell_Geneset_Scoring.R ├── Data ├── AMLCellType_Genesets.gmt ├── Cohort_Combined_Cytogenetics_Mutations_Feb16.csv ├── Cohort_Hierarchy_Genomic_Annotations.csv ├── Fig1_SingleCell_LSC │ ├── CIBERSORTx_GPR56_Fractions.csv │ ├── CIBERSORTx_LSC_Fractions.csv │ ├── CIBERSORTx_NKG2D_Fractions.csv │ ├── HSC_CyclePrimed_LSC_genesets.gmt │ ├── LSC_frequencies.csv │ └── h.all.v7.0.symbols.gmt ├── Fig2_Cohort_Deconvolution │ ├── BEAT_Clinical_anno.csv │ ├── CIBERSORTx_Results_BEAT.csv │ ├── CIBERSORTx_Results_Leucegene.csv │ ├── CIBERSORTx_Results_TARGET_pedAML.csv │ ├── CIBERSORTx_Results_TCGA.csv │ ├── Combination_Hierarchy.csv │ ├── Combination_Hierarchy_VAF25.csv │ ├── Induction_Failure │ │ ├── Annotation_InductionFailure_Chiu2019.csv │ │ ├── Annotation_InductionFailure_Herold2018.csv │ │ ├── CIBERSORTx_InductionFailure_Chiu2019_GSE103424.csv │ │ └── CIBERSORTx_InductionFailure_Herold2018_GSE106291.csv │ ├── Leucegene_combined_anno_cleaned.csv │ ├── Survival_Hierarchy_TCGA_BEAT_GSE6891.csv │ ├── TCGA_Clinical_anno.csv │ ├── pedAML_clinical_data.csv │ └── tcga_mutations.ipynb ├── Fig3_Relapse_Deconvolution │ ├── CIBERSORTx_DxRx_Christopher_2018.csv │ ├── CIBERSORTx_DxRx_Cocciardi_2019.csv │ ├── CIBERSORTx_DxRx_Li_2016.csv │ ├── CIBERSORTx_DxRx_Shlush_2017.csv │ └── scArches_PVG_Abbas_CellType_Classified.csv ├── Fig4_DrugResponse_LinClass7 │ ├── BEAT_AML_DrugResponses.csv │ ├── CIBERSORTx_Results_Lee2018_14refract_DrugScreen.csv │ ├── Lee2018_14ptx_refract_drugAUC.csv │ ├── Lee2018_30pt_DrugAUC.csv │ └── Lee2018_30pt_array.csv ├── Fig5_Literature_DrugResponse │ ├── CIBERSORTx_Results_KPT330_claire.csv │ ├── CIBERSORTx_Results_XPO1_KPT.csv │ ├── Cell_Line_Genomics.csv │ ├── Cell_Lines │ │ ├── CIBERSORTx_22d_HDAC8.csv │ │ ├── CIBERSORTx_5inhibitor_AF9.csv │ │ ├── CIBERSORTx_5inhibitor_nonAF9.csv │ │ ├── CIBERSORTx_AC4130_STAT5.csv │ │ ├── CIBERSORTx_ALRN6924_MDMXMDM2.csv │ │ ├── CIBERSORTx_ARV825OTX015_BET.csv │ │ ├── CIBERSORTx_ASLAN003_DHODH.csv │ │ ├── CIBERSORTx_ATHA_MYB.csv │ │ ├── CIBERSORTx_ATRATSA_RARAHDAC.csv │ │ ├── CIBERSORTx_AlCAr_PyrimidineSynthesis.csv │ │ ├── CIBERSORTx_Azacytidine_Hypometh.csv │ │ ├── CIBERSORTx_BRD_GSK3ab.csv │ │ ├── CIBERSORTx_CS_FTO.csv │ │ ├── CIBERSORTx_CX5461IBET151Doxorubicin_POLIBETTOPOII.csv │ │ ├── CIBERSORTx_DexaQuiz_FLT3.csv │ │ ├── CIBERSORTx_EPZ004777_DOT1L.csv │ │ ├── CIBERSORTx_EPZGSK_DOT1LEZH2_MOLM.csv │ │ ├── CIBERSORTx_EPZGSK_DOT1LEZH2_MV411.csv │ │ ├── CIBERSORTx_Entosplentinib_SYK.csv │ │ ├── CIBERSORTx_Etoposide_TOPOII.csv │ │ ├── CIBERSORTx_FB23_FTO.csv │ │ ├── CIBERSORTx_GSK3186000AGSK343_PRMT5EZH2.csv │ │ ├── CIBERSORTx_GSK690RN-1_KDM1A.csv │ │ ├── CIBERSORTx_IBET152_BET.csv │ │ ├── CIBERSORTx_INCB059872_LSD1.csv │ │ ├── CIBERSORTx_MB3GSKLSD1ATRA_GCN5LSD1RARA.csv │ │ ├── CIBERSORTx_MRT199665_PhosphoMEF2C.csv │ │ ├── CIBERSORTx_MitoCopper_MitoBlock6.csv │ │ ├── CIBERSORTx_NSC370284_TET1.csv │ │ ├── CIBERSORTx_OG86RAD001_LSD1MTORC1.csv │ │ ├── CIBERSORTx_OTX015_MTHFRBET.csv │ │ ├── CIBERSORTx_UNC1999_EZH.csv │ │ ├── CIBERSORTx_VTP50469_MeninMLL.csv │ │ └── CIBERSORTx_YKL_Palbociclib_BSJ_CDK6_Selective.csv │ ├── Drug_Cell_Line_pvalues.csv │ ├── Drug_Primary_pvalues.csv │ ├── GRCh38_transcript_lengths.txt │ ├── Primary │ │ ├── CIBERSORTx_AR42KPT9274_HDAC8NAMPT_Primary.csv │ │ ├── CIBERSORTx_AlCAr_PyrimidineSynthesis_Primary.csv │ │ ├── CIBERSORTx_AzaBay_HypomethIDH1_Primary.csv │ │ ├── CIBERSORTx_AzaGSK_HMALSD1_Primary.csv │ │ ├── CIBERSORTx_CrenolanibAza_FLT3Hypometh_Primary.csv │ │ ├── CIBERSORTx_Fx1_BCL6_Primary.csv │ │ ├── CIBERSORTx_JQ1CDKI-73_BETCDK9_Primary.csv │ │ ├── CIBERSORTx_KPT_XPO1_Primary.csv │ │ └── CIBERSORTx_TRC105_CD105_Primary.csv │ ├── hg19_transcript_lengths.txt │ └── pvg_AML_nuclear_export_AUCell.csv ├── Fig6_AML_PDX_Response │ ├── CC90009_ID_Conversion.csv │ ├── CIBERSORTx_Results_Cereblon.csv │ ├── CIBERSORTx_Results_JAK2.csv │ ├── CIBERSORTx_Results_LSCbulk.csv │ ├── Combo_CC90009_Fed_treatment_engraftment.csv │ ├── JAK2_CC90009_Clinical.csv │ ├── JAK2_sampledata.csv │ ├── LSCbulk_Primitive_NPM1status.csv │ ├── PDX_Response_CC90009.csv │ └── PDX_Response_Fedratinib.csv ├── Hierarchy_Reference_3Cohorts.h5ad └── scAML_new_annotations.csv ├── Fig_1.0a_scran_AML_HSCProg.R ├── Fig_1.0a_vanGalen_AML_scran_normalization.R ├── Fig_1.0b_pySCENIC_scAML.sh ├── Fig_1.1_LSPC_Reclustering_Characterization.ipynb ├── Fig_1.2_LSC_Analysis.ipynb ├── Fig_2.0_Cohort_Cluster_Survival.ipynb ├── Fig_2.1_Hierarchy_Genomic_Correlates.ipynb ├── Fig_2.2_Hierarchy_Survival.ipynb ├── Fig_3.0_Relapse_Deconvolution.ipynb ├── Fig_3.1_scRNA_Relapse_Abbas_et_al.ipynb ├── Fig_4.0_CellType_Drug_Correlations.ipynb ├── Fig_4.1_LinClass7_PC2_Regression.ipynb ├── Fig_5.0_Literature_Deconv_Processing.ipynb ├── Fig_5.1a_Literature_Deconv_Composition_UMAP.ipynb ├── Fig_5.1b_Literature_Deconv_Composition_Heatmaps.Rmd ├── Fig_5.2_Selinexor_Treatment.ipynb ├── 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