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broadinstitute
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cytominer_scripts
Scripts for processing morphological profiling data using cytominer
MIT License
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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