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Questions about using sc.read_csv

Open FionaMoon opened this issue 3 years ago • 0 comments

Hi, all As new to scanpy, I met strange things when using sc.read_csv, the obs are genes and the var are cells

adata = sc.read_csv(x)
data
# AnnData object with n_obs × n_vars = 41861 × 4270

The original csv is like this:

          bcETOJ bcHGXP bcIFJF bcDOFU bcGZTO bcHQXC bcGPUB  ... bcGFMJ bcCFYO bcGKZY bcIINI bcAPPS bcERNJ bcEJTY
rownames                                                    ...                                                 
5S_rRNA        0      0      0      0      0      0      0  ...      0      0      0      0      0      0      0
5_8S_rRNA      0      0      0      0      0      0      0  ...      0      0      0      0      0      0      0
7SK            0      0      0      0      0      0      0  ...      0      0      0      0      0      0      0
A1BG           0      0      0      0      0      0      0  ...      0      0      0      0      0      0      0
A1BG-AS1       0      0      0      0      0      0      0  ...      0      0      0      0      0      0      0
...          ...    ...    ...    ...    ...    ...    ...  ...    ...    ...    ...    ...    ...    ...    ...

Do I have to tranform dataframe every time using sc.read_csv ?

FionaMoon avatar Sep 16 '22 13:09 FionaMoon