Index contains duplicate entries, cannot reshape about swan_vis HOT 4 CLOSED

Hi, thanks for your kind words :)

I seem to recall debugging a similar problem for myself semi-recently. Can you tell me if you're using the latest commits from GitHub? If not, would you mind trying that?

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Yes, it should be the latest commit.

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OK, based on the warning you're getting from AnnData, it would appear that you have some duplicated transcript IDs, likely in your abundance matrix, judging by where the error is being thrown. To test this, please run one of the following code blocks in Python, depending on what format your data is in:

If you're using a TALON abundance file

import pandas as pd
df = pd.read_csv('<your abundance file>', sep='\t')
print(df.loc[df.annot_transcript_id.duplicated(keep=False)].sort_values(by='annot_transcript_id'))

If you're using the non-specific formatted abundance file:

import pandas as pd
df = pd.read_csv('<your abundance file>', sep='\t')
print(df.loc[df[df.columns[0]].duplicated(keep=False)].sort_values(by=[df.columns[0]]))

If this prints any data, you have duplicated transcript IDs in your dataset which you must address. Let me know if this helps you solve the problem, or if this code doesn't run for you (I did not test it).

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