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Some image.csv 's may have a few missing columns. However, because odo enforces a NOT NULL constraint on all columns, this throws an error.
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Take a look at the following function:
import pandas as pd
import polars as pl
import pyarrow as pa
import pyarrow.parquet as pq
from cytotable import convert
from parsl.config import Config
…
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The current implementation of sphering in pycytominer uses a constant value (`1e-6`) for the regularization parameter `epsilon`.
https://github.com/cytomining/pycytominer/blob/a5dac9e3fa3cdf61e9607…
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We want to address two issues here
1. define a new folder structure for profiling experiments
1. identify which of the components will be version controlled.
_I will update this comment periodica…
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`ImageNumber` is guaranteed to be unique only *within* an `Image.csv` but not across all `Image.csv` files in a dataset.
Does `pycytominer-transform` handle this correctly?
In [`cytominer-data…
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I am trying to collate csv files from a phenotypic screen into a single parquet or sqlite file using cytotable or cytominer (based on your suggestion). Some details on our study:
I have cellprofile…
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When reading the source code for `cytominer_eval.operations.precision_recall()` I noticed that the similarity_melted_df variable counts each replicate pair twice, e.g. A1 --> A2 and A2 --> A1.
This …
FloHu updated
3 years ago
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@michaelbornholdt presented an analysis on querying "hits" during profiling checkin today.
I'd love to be able to include this analysis in the LINCS complementarity paper. Michael estimated that hi…
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In #198 @d33bs states:
> Setting a goal post of when SQLite will be unsupported might help make some of the judgements surrounding what to do presently [specifically for handling memory leak #195]
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The only option is to define based on mean. I need to add an option to define based on median.