Source code for neuralee.dataset.seqfish

import pandas as pd
from .dataset import GeneExpressionDataset
import os


[docs]class SeqfishDataset(GeneExpressionDataset): def __init__(self, save_path='data/'): self.download_name = "SeqFISH.xlsx" self.save_path = save_path self.url = "https://www.cell.com/cms/attachment/2080562255/" \ "2072099886/mmc6.xlsx" data = self.download_and_preprocess() super().__init__( *GeneExpressionDataset.get_attributes_from_matrix(data))
[docs] def preprocess(self): print("Preprocessing dataset") xl = pd.ExcelFile(os.path.join(self.save_path, self.download_name)) ds = xl.parse("Hippocampus Counts") # They also used cell by genes print("Finished preprocessing dataset") return ds.values[:, 1:].astype(int)