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  • Remove samples rows from anndata - anndata - scverse
    Everything is connected, so you can’t remove rows from obs without removing rows from the whole object In your case you want to do one of the following: adata[adata obs["Region"] != "reg012"] adata[adata obs query("Region != 'reg012'") index] adata[[r != "reg012" for r in adata obs Region]]
  • python - remove sample from anndata . obs and . x - Stack Overflow
    I can see how to remove columns from anndata ie keep = ['a','b','c'] adata = adata [:, keep] How does one remove rows from anndata obs and anndata x? for example remove adata obs[Region='reg012'] Dataframe adata obs
  • deleting specific row · Issue #73 · scverse anndata - GitHub
    No, sorry, there is no way to delete a row as storage is in contiguous arrays you can do like this: t = adata obs drop(index=["C_DeepM_r_2_FRAS210239463_1r"]) adata= adata[adata obs["sample_index"] isin(t["sample_index"] to_list())]
  • Getting started with anndata — anndata 0. 13. 0. dev9+gee4ba21 documentation
    We can imagine this to be useful to subset the AnnData to particular cell types or gene modules of interest The rules for subsetting AnnData are quite similar to that of a Pandas DataFrame You can use values in the obs var_names, boolean masks, or cell index integers
  • AnnData clean up : r bioinformatics - Reddit
    Easiest would be to just make a new Anndata object with the attributes you want to keep Ask in scverse discourse
  • 5, maybe 10 minutes to AnnData - Adam Gayoso - Personal website
    We can imagine this to be useful to subset the AnnData to particular cell types or gene modules of interest The rules for subsetting AnnData are quite similar to that of a Pandas DataFrame You can use values in the obs var_names, boolean masks, or cell index integers
  • anndata. AnnData — anndata 0. 13. 0. dev7+gba27397 documentation
    AnnData stores a data matrix X together with annotations of observations obs (obsm, obsp), variables var (varm, varp), and unstructured annotations uns An AnnData object adata can be sliced like a DataFrame, for instance adata_subset = adata[:, list_of_variable_names] AnnData ’s basic structure is similar to R’s ExpressionSet [Huber15]
  • anndata - Annotated data — anndata 0. 11. 4 documentation
    anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray anndata offers a broad range of computationally efficient features including, among others, sparse data support, lazy operations, and a PyTorch interface





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