Reading and Writing

Write AnnData objects using its writing methods

write

Write AnnData objects to file.

Note

For reading annotation use pandas.read_… and add it to your AnnData object. The following read functions are intended for the numeric data in the data matrix X.

Read common file formats using

read	Read file and return AnnData object.

Read 10x formatted hdf5 files and directories containing .mtx files using

read_10x_h5	Read 10x-Genomics-formatted hdf5 file.
read_10x_mtx	Read 10x-Genomics-formatted mtx directory.
read_visium	Read 10x-Genomics-formatted visum dataset.

Read other formats using functions borrowed from anndata

read_h5ad	Read .h5ad-formatted hdf5 file.
read_csv	Read .csv file.
read_excel	Read .xlsx (Excel) file.
read_hdf	Read .h5 (hdf5) file.
read_loom	Read .loom-formatted hdf5 file.
read_mtx	Read .mtx file.
read_text	Read .txt, .tab, .data (text) file.
read_umi_tools	Read a gzipped condensed count matrix from umi_tools.