API¶
The central class:
AnnData([X, obs, var, uns, obsm, varm, …]) |
An annotated data matrix. |
Reading¶
Reading anndata’s native file format .h5ad.
read_h5ad(filename[, backed, chunk_size]) |
Read .h5ad-formatted hdf5 file. |
Reading other file formats.
read_csv(filename[, delimiter, …]) |
Read .csv file. |
read_excel(filename, sheet[, dtype]) |
Read .xlsx (Excel) file. |
read_hdf(filename, key) |
Read .h5 (hdf5) file. |
read_loom(filename[, sparse, cleanup, …]) |
Read .loom-formatted hdf5 file. |
read_mtx(filename[, dtype]) |
Read .mtx file. |
read_text(filename[, delimiter, …]) |
Read .txt, .tab, .data (text) file. |
read_umi_tools(filename[, dtype]) |
Read a gzipped condensed count matrix from umi_tools. |
read_zarr(store) |
Read from a hierarchical Zarr array store. |
Writing¶
Writing to anndata’s native file format .h5ad.
AnnData.write([filename, compression, …]) |
Write .h5ad-formatted hdf5 file. |
Writing to other formats.
AnnData.write_csvs(dirname[, skip_data, sep]) |
Write annotation to .csv files. |
AnnData.write_loom(filename[, write_obsm_varm]) |
Write .loom-formatted hdf5 file. |
AnnData.write_zarr(store, chunks) |
Write a hierarchical Zarr array store. |