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ktroule
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Add initial list of marker genes and a function to read.
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‎build/lib/sctools/__init_.py

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‎sctools/__init_.py ‎build/lib/sctools/__init__.py

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‎build/lib/sctools/metrics/soupy_ratio.py

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from joblib import Parallel, delayed
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import multiprocessing
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#import scanpy as sc
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#import pandas as pd
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import scanpy as sc
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import pandas as pd
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import glob
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import os
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‎build/lib/sctools/tools/__init__.py

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#!/usr/bin/env python
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from sctools.tools.pseudobulk_matrix import *
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from sctools.tools.load_markers import *
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__all__ = ["pseudobulk_matrix"]
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__all__ = ["pseudobulk_matrix", "load_markers", "src"]

‎build/lib/sctools/tools/load_markers.py

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import importlib_resources
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import pandas as pd
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def load_markers():
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my_resources = importlib_resources.files("sctools.tools") / "src"
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#text = (my_resources / "gene_markers.csv").read_text()
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#template = importlib.resources.read_text("tools.src", "gene_markers.csv")
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return(pd.read_csv((my_resources / "gene_markers.csv")))

‎build/lib/sctools/tools/src/__initi__.py

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from tools.src import *

‎build/lib/sctools/tools/src/gene_markers.csv

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Gene,Cell,Group
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DCN,Mesenchymal,
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TCF21,Mesenchymal,
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PDGFRA,Mesenchymal,
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COL1A1,Mesenchymal,
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PTCH1,Theca lineage,
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STC1,Theca lineage,
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ESR2,Theca lineage,
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APOC1,Theca lineage,
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NR5A1,Theca lineage,
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PTCH2,Theca lineage,
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MEST,Theca lineage,
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WFDC1,Theca lineage,
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TIAM1,Theca lineage,
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CLDN1,pre-Theca,
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GLI1,pre-Theca,
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PIEZO2,pre-Theca,
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KCNT1,Theca,
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CALB2,Theca,
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INHA,Theca,
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GSTA1,Theca,
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MAP3K15,Theca,
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LHCGR,Theca LHCGR,
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INSL3,Theca steroidogenic,
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ANPEP,Theca steroidogenic,
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HSD3B2,Theca steroidogenic,
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CYP17A1,Theca steroidogenic,
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MGST1,Theca steroidogenic,
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HGF,Theca HGF,
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LHX9,Ovarian stroma,
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TCF21,Ovarian stroma,
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OGN,Ovarian stroma,
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AFF3,Stroma sign,
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IL1RAPL1,Stroma sign,
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SGCZ,Stroma sign,
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PWRN1,Stroma sign,
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CDK13,Stroma sign,
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COLEC11,Stroma preTheca,
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LAMB1,Stroma preTheca,
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TRABD2A,Stroma WNT4,
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TMEM100,Stroma WNT4,
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WNT4,Stroma WNT4,
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COL10A1,Stroma WNT4,
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COL8A1,Stroma WNT4,
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SST,sPAX8,
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CALY,sPAX8,
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CXCR4,sPAX8,
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PLAU,sPAX8,
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PAX8,sPAX8,
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FST,sPAX8,
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LHX9,gonadal,
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ARX,gonadal,
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GATA4,gonadal,
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GATA2,extragonadal,
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RSPO3,extragonadal,
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NR2F1,extragonadal,
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IGFBP6,Fib C3,
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NR2F1,Fib C3,
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GATA2,Fib C3,
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BCHE,Fib C3,
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RSPO3,Fib C3,
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C3,Fib C3,
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MCAM,PV lineage,
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RGS5,PV lineage,
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ACTA2,PV lineage,
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MYH11,PV lineage,
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SMTNL2,ePV STEAP4,
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STEAP4,ePV STEAP4,
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SSTR2,ePV STEAP4,
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ARHGAP15,ePV STEAP4,
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MMP11,ePV MMP11,
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LPL,ePV MMP11,
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TDO2,ePV MMP11,
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CYGB,ePV MMP11,
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MAP3K7CL,ePV AOC3,
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AOC3,ePV AOC3,
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CCND1,ePV AOC3,
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SLC38A11,ePV AOC3,
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OR51E1,ePV AOC3,
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FNDC1,ePV AOC3,
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MYOM2,ePV AOC3,
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NRARP,ePV AOC3,
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KCNAB1,mPV MYH11,
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FHL5,mPV MYH11,
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RERGL,mPV MYH11,
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LEFTY2,uSMCs,
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ITGA11,uSMCs,
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ACTG2,uSMCs,
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PTPRC,Immune,
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CD3D,Lymphoid,
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NKG7,Lymphoid,
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NCAM1,Lymphoid,
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CSF1R,Myeloid,
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CD14,Myeloid,
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CDH5,Endothelial,
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PECAM1,Endothelial,
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VWF,Endothelial,
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CXCR4,Endo_arte,
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PRND,Endo_arte,
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GJA4,Endo_arte,
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PLVAP,Endo_fenestrated,
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APLNR,Endo_fenestrated,
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PLAT,Endo_fenestrated,
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PROX1,Endo_lymphatic,
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CCL21,Endo_lymphatic,
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RELN,Endo_lymphatic,
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OIT3,Endo_venous,
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ECM1,Endo_venous,
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SPP1,Endo_venous,
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KRT19,Epithelial,
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EPCAM,Epithelial,
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HBA1,Erythroid,
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GYPC,Erythroid,
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PLP1,Neural,
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ELAVL4,Neural,
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ASCL1,Neural,
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MPZ,Neural,
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CHL1,Neural,
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DDX4,GCs,
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DAZL,GCs,
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FIGLA,oocyte,
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GDF9,oocyte,
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NOBOX,oocyte,
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ZP3,oocyte,
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ARG2,secondary oocyte,
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UPK3B,OSE,
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KLK11,OSE,
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LRRN4,OSE,
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KLF10,theca Primordial arrested,
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IRF1,theca Primordial arrested,
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MAFF,theca Primordial arrested,
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KLF2,theca Primordial arrested,
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INHBB,Inhibins,
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INHA,Inhibins,
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INHBA,Inhibins,
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DDIT4,Stress,
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GADD45B,Stress,
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SERTAD1,Stress,
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DDIT3,Stress,
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CDKN1A,Stress,
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BTG2,Stress,
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NR4A2,Stress,
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ATF3,Stress,
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SOCS3,Stress,
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HSPA1A,Stress,
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NPHS2,Glomerular mesonephros,
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PTPRO,Glomerular mesonephros,
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CLIC5,Glomerular mesonephros,
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MKI67,cycling,
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CDK1,cycling,
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TOP2A,cycling,
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MALAT1,lncRNA,
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XIST,lncRNA,
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NEAT1,lncRNA,
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HTRA1,Granulosa cumulus - antral follicle,
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IGFBP2,Granulosa cumulus - antral follicle,
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IHH,Granulosa cumulus - antral follicle,
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INHBB,Granulosa cumulus - antral follicle,
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FSHR,Granulosa FSH responsive,
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AKIRIN1,Granulosa mural - antral follicle,
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CITED2,Granulosa mural - antral follicle,
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LIPH,Granulosa mural - antral follicle,
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EGR4,Granulosa mural - antral follicle,
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KRT18,Granulosa mural - antral follicle,
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AMH,Granulosa early - primary follicle,
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FST,Granulosa early - primary follicle,
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GSTA1,Granulosa early - primary follicle,
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HSD17B1,Granulosa early - primary follicle,
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INHBB,Granulosa early - primary follicle INHBB+,
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LRP8,Granulosa early - primary follicle INHBB+,
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VCAN,Granulosa early - primary follicle INHBB+,
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HES4,Granulosa squamous (primordial follicle),
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LHX2,Granulosa squamous (primordial follicle),
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NOTCH3,Granulosa squamous (primordial follicle),
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NR1H4,Granulosa squamous (primordial follicle),
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RDH10,Granulosa squamous (primordial follicle),
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CDH1,Granulosa squamous (primordial follicle),
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FSHR,granulosa FSH responsive,
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AMH,granulosa Primary a,
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HSD17B1,granulosa Primary a,
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FST,granulosa Primary a,
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LRP8,granulosa Primary b,
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INHBB,granulosa Primary b,
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VCAN,granulosa Primary b,
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GSTA1,granulosa Primary b,
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ZFPM2,granulosa preAntral,
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BMPR2,granulosa preAntral,
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BMPR1A,granulosa preAntral,
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BMPR1B,granulosa preAntral,
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ATM,granulosa preAntral,
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UBR2,granulosa preAntral,
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WIPF3,granulosa,
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GATA4,granulosa,
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WNT6,granulosa early,
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FOXL2,granulosa early,
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INHA,granulosa early,
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HES4,granulosa Primordial fetal,
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LHX2,granulosa Primordial fetal,
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NOTCH3,granulosa Primordial fetal,
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HEYL,granulosa Primordial fetal,
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RDH10,granulosa Primordial fetal,
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NR1H4,granulosa Primordial fetal,
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ARX,Ovarian somatic,
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GATA4,Ovarian somatic,
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COLEC11,Stroma theca precursor,
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LAMB1,Stroma theca precursor,
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GLI1,Theca externa,
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THBD,Theca externa,
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CLDN1,Theca externa,
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APOD,Theca externa,
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PIEZO2,Theca externa,
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KCNT1,Theca interna,
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CALB2,Theca interna,
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INHA,Theca interna,
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GSTA1,Theca interna,
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CYP11A1,Theca interna,
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MAP3K15,Theca interna,

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