Installation

I recommend using Miniconda to manage packages and creating an entirely new environment to install scanpy.

conda install -c conda-forge scanpy python-igraph leidenalg

Basic conception before your start

AnnData class

An "AnnData" class is the interface to the Scanpy operation, meaning we must create an AnnData object as a parameter to the Scanpy function.

At the most basic level, an AnnData object adata stores a data matrix adata.X, annotation of observations adata.obs and variables adata.var as pd.DataFrame and unstructured annotation adata.uns as dict. Names of observations and variables can be accessed via adata.obs_names and adata.var_names, respectively. AnnData objects can be sliced like dataframes, for example, adata_subset = adata[:, list_of_gene_names]

import scanpy as sc
import os
adata = sc.read_csv('../data/GSM5226574_C51ctr_raw_counts.csv').T
adata

Let's see the properties of AnnData.

type(adata) 
type(adata.X)
adata.var #extract var(python DataFrame object that describe genes)
adata.obs #extract observations(python DataFrame object that describe cells)

adata.var_names #return an index objects of gene names
adata.obs_names #return an index objects of cell barcodes