nf1_schwann_cell_morphology_signature - Manuscript second round revisions

What's Changed

• Add new DOI by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/92
• Update and add figures per manuscript review by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/93
• Fixing whitespace issues in main fig 1 by @gwaybio in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/94
• Fix figure 7 by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/95

Full Changelog: https://github.com/WayScience/nf1schwanncellmorphologysignature/compare/v1.2...v1.3

- Jupyter Notebook
Published by jenna-tomkinson 7 months ago

nf1_schwann_cell_morphology_signature - Manuscript ready

In this release, all changes and analysis performed prepared the repository to be ready for manuscript after response to reviewers.

What's Changed

• Add updated doi and update title in readme by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/73
• Update Figure 1B by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/75
• Split figure 4 and generate figure 5 by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/76
• Generate main figure 6 and rename figures folder by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/78
• Add ks test and update figure 6 by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/79
• Add qc supp figure by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/80
• Rerun analysis with QC data by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/81
• Rerun QC model and main figures only by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/82
• Update supp figures by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/83
• Update single cell QC figure by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/84
• Update roc auc analysis by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/85
• Update ks test and roc auc analysis by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/86
• Update LICENSE by @MattsonCam in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/74
• Add new supplemental figure 5 by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/87
• Update main README by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/88
• Update readme for accuracy by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/89
• Final updates by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/90
• Add citation file and update README by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/91

Full Changelog: https://github.com/WayScience/nf1schwanncellmorphologysignature/compare/v1.1...v1.2

- Jupyter Notebook
Published by jenna-tomkinson 10 months ago

nf1_schwann_cell_morphology_signature - v1.1 - Manuscript Updates

Release to update figures for the manuscript based on collaborator reviews.

What's Changed

• Add minted DOI by @MattsonCam in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/71
• Update manuscript figures per review by @jenna-tomkinson in https://github.com/WayScience/nf1schwanncellmorphologysignature/pull/72

Full Changelog: https://github.com/WayScience/nf1schwanncellmorphologysignature/compare/v1.0...v1.1

- Jupyter Notebook
Published by jenna-tomkinson over 1 year ago

nf1_schwann_cell_morphology_signature - 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 https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/1
• Preprocessing, visualization, and eda with obnibus and post hoc testing by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/2
• Model training, evaluation, and interpretation by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/3
• Dev best features by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/4
• Linear model creation and interpretation by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/5
• Retraining and interpreting logistic regression by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/6
• Plate classifications by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/7
• Plate projections by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/8
• Construct correlations plate 4 by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/9
• Median construct correlations plate 4 by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/10
• Bulk construct correlations plate 4 by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/12
• Bulk correlations no treatment by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/13
• Single cell correlations no treatment by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/14
• Post feature selection correlation analysis by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/15
• Updated conda environment by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/16
• Classify genotypes for plate 4 by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/17
• Plot precision recall curves plate 4 by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/18
• Classify genotypes plates 3 3p by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/19
• Refactor plates 3 3p genotype classification by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/20
• Plate 5 aggregating cells and correlating wells by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/22
• Subset sum test well sampling strategy by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/23
• Generate Supplemental Figure 2 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/25
• Updated Well Sampling by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/27
• Update correlation util and plate 5 correlation analysis by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/29
• Optimize logistic regression plates 3, 3 prime, and 5 by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/28
• Evaluate Plate Model Performance by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/30
• Compute shuffled model data by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/31
• Generated shuffled model evaluation data by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/32
• Add main figure 1 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/34
• Train final nf1 model by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/33
• Evaluated performance of the nf1 genotype classification model by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/35
• Update plate 5 correlations post aggregation by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/38
• Train final nf1 model by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/37
• Update plate 4 correlations after well aggregation by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/39
• Evaluated performance of the nf1 genotype classification model by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/40
• Compute sirna-treated cell genotype probabilities with updated model by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/41
• Add bulk correlation figure from plate 4 analysis by @gwaybio in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/11
• Add main figure 3 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/42
• Add main figure 5 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/43
• Add main figure 2 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/44
• Add main figure 4 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/45
• Retrain NF1 model after plate 3 prime name bug fix by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/46
• Evaluated NF1 model after plate 3 prime name bug fix by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/47
• Retrainined NF1 model without plate 4 cell data by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/49
• Updated the evaluation results after NF1 model retraining by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/50
• Update main figure 1 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/51
• Remove older analysis by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/52
• Update readmes and simplify repo by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/53
• Update main figure 2 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/54
• Update main figure 3 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/55
• Update plate correlation analysis by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/56
• Update main figure 4 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/61
• Update main README by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/65
• Cell Count EDA of NF1 single-cell plate data by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/60
• Updated NF1 data submodule by @MattsonCam in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/66
• Update main figures 1, 2, and 4 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/67
• Generate supplemental figure 1 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/68
• Add supp fig 2 by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/69
• Add figure READMEs and bash scripts by @jenna-tomkinson in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/70

New Contributors

• @MattsonCam made their first contribution in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/1
• @jenna-tomkinson made their first contribution in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/25
• @gwaybio made their first contribution in https://github.com/WayScience/NF1SchwannCelldata_analysis/pull/11

Full Changelog: https://github.com/WayScience/NF1SchwannCelldata_analysis/commits/v1.0

- Jupyter Notebook
Published by MattsonCam over 1 year ago