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Collating possible solutions from the answers:
For IN: df[df['A'].isin([3, 6])]
df[df['A'].isin([3, 6])]
For NOT IN:
df[-df["A"].isin([3, 6])]
df[~df["A"].isin([3, 6])]
df[df["A"].isin([3, 6]) == False]
df[np.logical_not(df["A"].isin([3, 6]))]