broadinstitute cytominer_scripts issues

broadinstitute / cytominer_scripts

Scripts for processing morphological profiling data using cytominer

MIT License

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issues

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Parameterize aggregate, copying from cytotools

#36 shntnu closed 4 years ago
2
Specify compartments to aggregate via commandline parameter

#35 shntnu closed 4 years ago
1
`annotate.R` fails when plate name has underscores in it

#34 bethac07 opened 5 years ago
3
Resolve `evaluation nested too deeply` issues

#33 shntnu closed 5 years ago
1
[WIP] Add script to capture heterogeneity

#32 gwaybio opened 5 years ago
2
Specify isolated vs. colony definition

#31 gwaybio opened 5 years ago
1
[WIP] Option for isolated and colony profiles

#30 shntnu opened 5 years ago
3
Enable option to create profiles for isolated and colony cells

#29 shntnu opened 5 years ago
0
`sample.R` fails with integer metadata

#28 gwaybio opened 5 years ago
0
`preselect.R` for replicate_correlation does not use subset rows

#27 gwaybio opened 5 years ago
0
Confusing Error in `preselect.R`

#26 gwaybio closed 5 years ago
1
Adding custom `--null_quantile` flag in audit

#25 gwaybio opened 5 years ago
1
`audit.R` Custom Null Threshold Quantile in Audit

#24 gwaybio opened 5 years ago
0
Use median instead of mean - a hack!

#23 shntnu closed 6 years ago
0
Delete process.sh and related files

#22 shntnu closed 6 years ago
1
Add option to have collate download CSV files

#21 shntnu closed 6 years ago
0
Add option to have collate download CSV files

#20 shntnu closed 6 years ago
1
Change default aggregation to be mean instead of median

#19 shntnu closed 6 years ago
0
Change default aggregation to be mean instead of median

#18 shntnu closed 6 years ago
0
Remove Image_ prefix

#17 shntnu closed 6 years ago
0
Remove `Image_` prefix

#16 shntnu closed 6 years ago
1
Replace `row_number` with `dense_rank`

#15 shntnu closed 7 years ago
1
Update preselect.R

#14 shntnu closed 7 years ago
1
Change cytominer::select to cytominer::variable_select

#13 shntnu closed 7 years ago
1
Should backend creation use first image set as a "template"?

#12 bethac07 closed 7 years ago
1
Implement normalize.quantiles as preprocessing

#11 shntnu closed 7 years ago
1
Update annotate.R

#10 shntnu closed 7 years ago
0
`annotate.R` Don't let command line param override specifications of metadata file

#9 shntnu opened 7 years ago
0
`preselect.R` Don't assume multiple identical plates

#8 bethac07 opened 7 years ago
2
Issue/6

#7 cells2numbers closed 7 years ago
0
poor estimation of the threshold used in audit.R due to limited sample size

#6 cells2numbers closed 7 years ago
1
`aggregate` should handle QC columns

#5 shntnu closed 7 years ago
1
Aggregate should also include per_image features

#4 shntnu closed 7 years ago
1
Store profiles in a directory different from backend

#3 shntnu opened 7 years ago
0
Implement QC functions for profiling

#2 shntnu opened 7 years ago
3
Create option to explicitly specify all paths

#1 shntnu closed 7 years ago
3