broadinstitute pooled-cell-painting-profiling-recipe issues

broadinstitute / pooled-cell-painting-profiling-recipe

:woman_cook: Recipe repository for image-based profiling of Pooled Cell Painting experiments

BSD 3-Clause "New" or "Revised" License

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issues

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Data split error in summarize-cells

#96 ErinWeisbart opened 2 weeks ago
0
QC plots: DAPI correlation in Nuclei

#95 ErinWeisbart opened 3 months ago
0
Pandas-2-ize the recipe

#94 bethac07 opened 9 months ago
0
Add optional extra barcode preprocessing

#93 ErinWeisbart opened 9 months ago
1
add salvage cell categorization method

#92 ErinWeisbart opened 9 months ago
0
Create normalized single_cell_profiles_by_guide output

#91 ErinWeisbart closed 9 months ago
14
add skip counter to 0.merge-single-cells

#90 ErinWeisbart closed 2 years ago
0
Handle missing metadata

#89 ErinWeisbart closed 2 years ago
1
Change Skip Site/Overwrite Behavior in 0.preprocess-sites

#88 ErinWeisbart opened 2 years ago
0
create logger

#87 ErinWeisbart closed 2 years ago
2
additional output for easy NGS comparison Total_Barcode_Calls_Counts

#86 ErinWeisbart closed 2 years ago
0
relevant configs are now in template not recipe

#85 ErinWeisbart closed 2 years ago
0
Config mismatch between recipe and template

#84 ErinWeisbart closed 2 years ago
1
handle pandas parse error

#83 ErinWeisbart closed 2 years ago
5
Codify new contribution protocol

#82 ErinWeisbart closed 9 months ago
8
Make folders only when necessary

#81 ErinWeisbart opened 2 years ago
0
add print statements at beginning and end of modules

#80 ErinWeisbart closed 2 years ago
0
Skip corrupted site files

#79 gwaybio closed 2 years ago
1
add a configurable chunksize whenever loading

#78 bethac07 closed 2 years ago
16
Add output file specifically for comparison to NGS data.

#77 ErinWeisbart closed 2 years ago
1
Hardcoding Cells and Nuclei for threshold QC

#76 gwaybio opened 3 years ago
0
enable multi plate handling for qc

#75 ErinWeisbart closed 3 years ago
1
4.image-and-segmentation-qc.py should produce figures on a per-plate basis

#74 ErinWeisbart closed 3 years ago
3
Error in 4.image-and-segmentation-qc.py

#73 gwaybio opened 3 years ago
2
update qc section of recipe

#72 ErinWeisbart closed 3 years ago
2
Update recipe to handle custom user data splitting

#71 gwaybio closed 3 years ago
0
Add functionality to combine aggregated site files

#70 gwaybio opened 3 years ago
0
Aggregate fails when output_single_file_only option set to False

#69 gwaybio opened 3 years ago
1
Add step arguments to all recipe scripts

#68 gwaybio closed 3 years ago
0
Remove hardcoded site info

#67 gwaybio closed 3 years ago
0
Cell count file is outputting NaN for plate, well, and site_location columns

#66 gwaybio closed 3 years ago
0
Adding cell quality scoring using the Feldman et al. method to recipe

#65 gwaybio opened 3 years ago
1
Bug fixes and adding "perform" flags to all scripts

#64 gwaybio closed 3 years ago
0
Convert quality_col to list

#63 hillsbury closed 3 years ago
0
Add load_features import

#62 gwaybio closed 3 years ago
0
Barcode controls missing from guide abundance summary (cell count per perturbation)

#61 hillsbury closed 3 years ago
0
Maintaining different versions of recipe

#59 hillsbury closed 2 years ago
2
add cell count per perturbation summary

#58 hillsbury closed 3 years ago
0
Single cell normalization enhancement option

#57 gwaybio opened 3 years ago
1
Include summary step for guide + guide abundances (cell count per perturbation)

#56 gwaybio opened 3 years ago
12
Minor updates

#55 gwaybio closed 3 years ago
0
update correlation qc

#54 ErinWeisbart closed 3 years ago
1
Updating recipe to work with new configuration file setup

#53 gwaybio closed 3 years ago
1
Add logger to capture weld parameters, warnings, and errors

#52 gwaybio closed 2 years ago
0
Remove example_site requirement in prefilter feature config

#51 gwaybio closed 3 years ago
2
Add multi-plate option

#50 gwaybio closed 3 years ago
1
Adding sanitizer for gene column

#49 gwaybio closed 3 years ago
0
Sanitize gene column

#48 gwaybio closed 3 years ago
0
Add print statements

#46 gwaybio closed 2 years ago
1
Revert `site_full` back to `site`

#45 gwaybio closed 3 years ago
5