In scanpy, there is a function to directly read in the csv file as an anndata object (https://scanpy.readthedocs.io/en/stable/generated/scanpy.read_csv.html). This assumes that your columns are genes and your rows are cells.

If your pandas data frame is not that huge, you can also convert it like:

import scanpy as sc

import pandas as pd

import anndata as ad

import numpy as np

from scipy.sparse import csr_matrix

## example df

df = pd.DataFrame(

np.random.poisson(1, size=(100, 2000)),

columns=["gene" + str(i) for i in range(2000)],

index = ["cell" + str(i) for i in range(100)]

)

## make sure it takes on a sparse matrix

## provide gene and cell names

adata = ad.AnnData(csr_matrix(df.values))

adata.obs_names = df.index

adata.var_names = df.columns

Thank you so much, Gen Lin ! This is exactly what I was looking for.

Myles Joshua Toledo Tan Converting a.csv file to an AnnData file for use in Scanpy is a simple procedure. Here's an example of how it may be done:

1. You must first install the anndata package, which can be done by typing pip install anndata into your command line.

2. Following that, import the relevant libraries, such as pandas and anndata.

import pandas as pd

import anndata

3. Then, using the pd.read csv() method, read your.csv file into a pandas DataFrame.

data = pd.read_csv("your_file.csv")

4. After that, you can use the anndata.AnnData() method to convert the DataFrame to an AnnData object.

adata = anndata.AnnData(data)

5. Finally, you may use the scanpy library's different methods to conduct any extra processing or analysis on your AnnData object.

It's worth noting that when you convert a dataframe to an AnnData object, it thinks the rows are observations and the columns are variables. If you have the inverse, use.T to transpose the dataframe.

You can alternatively use scanpy.read csv() to directly import the csv file into an AnnData object to get the same result.

adata = sc.read_csv("your_file.csv")

Please let me know if there is anything else I can do for you.

Hi, please check the methods of the following recent research paper:

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