v1.0 - Manuscript Submission

Full version release for analyzing NF1 genotype morphologies, as well as training, evaluating, and validating machine learning models to predict NF1 genotypes from single-cell morphology representations.

What's Changed

• Added first analysis and classification code by @MattsonCam in #1
• Preprocessing, visualization, and eda with obnibus and post hoc testing by @MattsonCam in #2
• Model training, evaluation, and interpretation by @MattsonCam in #3
• Dev best features by @MattsonCam in #4
• Linear model creation and interpretation by @MattsonCam in #5
• Retraining and interpreting logistic regression by @MattsonCam in #6
• Plate classifications by @MattsonCam in #7
• Plate projections by @MattsonCam in #8
• Construct correlations plate 4 by @MattsonCam in #9
• Median construct correlations plate 4 by @MattsonCam in #10
• Bulk construct correlations plate 4 by @MattsonCam in #12
• Bulk correlations no treatment by @MattsonCam in #13
• Single cell correlations no treatment by @MattsonCam in #14
• Post feature selection correlation analysis by @MattsonCam in #15
• Updated conda environment by @MattsonCam in #16
• Classify genotypes for plate 4 by @MattsonCam in #17
• Plot precision recall curves plate 4 by @MattsonCam in #18
• Classify genotypes plates 3 3p by @MattsonCam in #19
• Refactor plates 3 3p genotype classification by @MattsonCam in #20
• Plate 5 aggregating cells and correlating wells by @MattsonCam in #22
• Subset sum test well sampling strategy by @MattsonCam in #23
• Generate Supplemental Figure 2 by @jenna-tomkinson in #25
• Updated Well Sampling by @MattsonCam in #27
• Update correlation util and plate 5 correlation analysis by @MattsonCam in #29
• Optimize logistic regression plates 3, 3 prime, and 5 by @MattsonCam in #28
• Evaluate Plate Model Performance by @MattsonCam in #30
• Compute shuffled model data by @MattsonCam in #31
• Generated shuffled model evaluation data by @MattsonCam in #32
• Add main figure 1 by @jenna-tomkinson in #34
• Train final nf1 model by @MattsonCam in #33
• Evaluated performance of the nf1 genotype classification model by @MattsonCam in #35
• Update plate 5 correlations post aggregation by @MattsonCam in #38
• Train final nf1 model by @MattsonCam in #37
• Update plate 4 correlations after well aggregation by @MattsonCam in #39
• Evaluated performance of the nf1 genotype classification model by @MattsonCam in #40
• Compute sirna-treated cell genotype probabilities with updated model by @MattsonCam in #41
• Add bulk correlation figure from plate 4 analysis by @gwaybio in #11
• Add main figure 3 by @jenna-tomkinson in #42
• Add main figure 5 by @jenna-tomkinson in #43
• Add main figure 2 by @jenna-tomkinson in #44
• Add main figure 4 by @jenna-tomkinson in #45
• Retrain NF1 model after plate 3 prime name bug fix by @MattsonCam in #46
• Evaluated NF1 model after plate 3 prime name bug fix by @MattsonCam in #47
• Retrainined NF1 model without plate 4 cell data by @MattsonCam in #49
• Updated the evaluation results after NF1 model retraining by @MattsonCam in #50
• Update main figure 1 by @jenna-tomkinson in #51
• Remove older analysis by @MattsonCam in #52
• Update readmes and simplify repo by @MattsonCam in #53
• Update main figure 2 by @jenna-tomkinson in #54
• Update main figure 3 by @jenna-tomkinson in #55
• Update plate correlation analysis by @MattsonCam in #56
• Update main figure 4 by @jenna-tomkinson in #61
• Update main README by @jenna-tomkinson in #65
• Cell Count EDA of NF1 single-cell plate data by @MattsonCam in #60
• Updated NF1 data submodule by @MattsonCam in #66
• Update main figures 1, 2, and 4 by @jenna-tomkinson in #67
• Generate supplemental figure 1 by @jenna-tomkinson in #68
• Add supp fig 2 by @jenna-tomkinson in #69
• Add figure READMEs and bash scripts by @jenna-tomkinson in #70

New Contributors

• @MattsonCam made their first contribution in #1
• @jenna-tomkinson made their first contribution in #25
• @gwaybio made their first contribution in #11

Full Changelog: https://github.com/WayScience/NF1_SchwannCell_data_analysis/commits/v1.0