angelolab TNBC_python_scripts issues

angelolab / TNBC_python_scripts

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Estimating false positives ()

#74 camisowers closed 3 weeks ago
0
Timepoint name fixes found in figure/supplementary scripts

#73 camisowers closed 2 months ago
1
Semi-final cleanup

#72 ngreenwald closed 3 months ago
0
Readme updates

#71 camisowers closed 3 months ago
0
Switch to FDR p-value and remove Localization

#70 camisowers closed 3 months ago
0
Average cell counts per timepoint plots

#69 camisowers closed 3 months ago
0
Figure tweaks

#68 ngreenwald closed 3 months ago
0
Paper tweaks

#67 ngreenwald closed 4 months ago
0
minor tweaks in the feature order heatmaps

#66 jranek closed 4 months ago
0
Immune_agg compartment and Clinical_benefit adjustments

#65 camisowers closed 4 months ago
0
Supplemental figure tweaks

#64 ngreenwald closed 4 months ago
0
Feature evolution style changes

#63 jranek closed 4 months ago
0
Reorganization part 2

#62 ngreenwald closed 4 months ago
0
Compartment-specific feature differences

#61 camisowers closed 4 months ago
0
Reorganize supplementary plotting

#60 ngreenwald closed 4 months ago
0
Minor tweaks after re-run

#59 camisowers closed 4 months ago
0
Rename and organize main figures

#58 ngreenwald closed 5 months ago
0
Outlier analysis

#57 jranek closed 5 months ago
0
Plot feature differences by timepoint

#56 jranek closed 5 months ago
0
Compute the correlation between response-associated features

#55 jranek closed 5 months ago
0
Masking path adjustments

#54 camisowers closed 5 months ago
0
move code for generating image-level clusters back to main pipeline

#53 ngreenwald closed 5 months ago
0
Standardize channel normalization params across panel validation visualizations

#52 alex-l-kong closed 5 months ago
0
supplementary tables

#51 ngreenwald closed 5 months ago
0
Outcomes supplement

#50 ngreenwald closed 6 months ago
0
Tweak feature tuning visualizations

#49 alex-l-kong closed 5 months ago
0
Update `validate_panel` normalization method to use cohort-wide constants per channel

#48 alex-l-kong opened 6 months ago
0
Genomics supplementary figures

#47 ngreenwald closed 6 months ago
0
Incorporate spatial organization into pipeline

#46 ngreenwald opened 6 months ago
0
Multivariate feature plots

#45 ngreenwald closed 6 months ago
1
Re-run analysis with updated parameters

#44 camisowers closed 5 months ago
1
Next steps for feature extraction pipeline

#43 ngreenwald opened 7 months ago
0
Random tweaks

#42 ngreenwald closed 7 months ago
1
Supplementary plots part 3

#41 ngreenwald closed 3 months ago
0
HnE Core, FOV, Segmentation Overlay Plots

#40 srivarra closed 7 months ago
0
Estimating false positives

#39 camisowers closed 7 months ago
0
Generate hyperparameter tuning plots for specific features

#38 alex-l-kong closed 6 months ago
0
New genomics

#37 ngreenwald closed 8 months ago
0
Feature extraction parameter tuning tests

#36 alex-l-kong closed 6 months ago
15
Rna seq comparisons

#35 camisowers closed 8 months ago
0
Cell Identification and Classification - Segmentation Plots

#34 srivarra closed 7 months ago
3
Subdirectory for cluster plots

#33 ngreenwald closed 8 months ago
0
Generate a stitched image of a pre- and post-Rosetta channel, along with source

#32 alex-l-kong closed 7 months ago
0
Create comparisons of normalized_mean features between different timepoints

#31 alex-l-kong closed 7 months ago
1
Define and visualize occupancy statistic metrics

#30 alex-l-kong opened 9 months ago
0
Plot cell proportions by timepoint

#29 camisowers closed 8 months ago
0
Integrate genomics comparisons

#28 ngreenwald closed 9 months ago
0
Supplementary plots part 2

#27 ngreenwald closed 3 months ago
0
QC batch effects supplementary figure

#26 camisowers closed 9 months ago
0
Individual files

#25 ngreenwald closed 10 months ago
0