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broadinstitute
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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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Something buggy in 0.preprocess-sites/0.prefilter-features.py
#97
ErinWeisbart
opened
3 months ago
0
Data split error in summarize-cells
#96
ErinWeisbart
opened
3 months ago
0
QC plots: DAPI correlation in Nuclei
#95
ErinWeisbart
opened
6 months ago
0
Pandas-2-ize the recipe
#94
bethac07
opened
1 year ago
0
Add optional extra barcode preprocessing
#93
ErinWeisbart
opened
1 year ago
1
add salvage cell categorization method
#92
ErinWeisbart
opened
1 year ago
0
Create normalized single_cell_profiles_by_guide output
#91
ErinWeisbart
closed
1 year 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
1 year 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
3 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
4 years ago
0
update correlation qc
#54
ErinWeisbart
closed
4 years ago
1
Updating recipe to work with new configuration file setup
#53
gwaybio
closed
4 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
4 years ago
2
Add multi-plate option
#50
gwaybio
closed
4 years ago
1
Adding sanitizer for gene column
#49
gwaybio
closed
4 years ago
0
Sanitize gene column
#48
gwaybio
closed
4 years ago
0
Add print statements
#46
gwaybio
closed
2 years ago
1
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