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Bishop-Laboratory
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autoPLIER-analysis
Analysis for the autoPLIER project
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Latent space algebra
#55
millerh1
opened
1 year ago
1
Comparison matrix vs NMF, PLIER, PCA, scVI
#54
millerh1
opened
1 year ago
1
Retry with KEGG
#53
millerh1
opened
1 year ago
0
Testing AP on PBMC data with KEGG
#52
millerh1
opened
1 year ago
1
LV interpretability
#51
Julian-Borbeck
opened
2 years ago
2
Identifiability problem
#50
millerh1
closed
1 year ago
2
Experiment: Differentiation of HSCs
#49
millerh1
opened
2 years ago
0
Could use this method unsupervised for cluster marker analysis
#48
millerh1
opened
2 years ago
0
Get pathway contributions to classification
#47
millerh1
opened
2 years ago
0
Plot ideas
#46
millerh1
opened
2 years ago
0
Port Jupyter Notebooks to Colab
#45
millerh1
opened
2 years ago
0
COVID analysis (biological story)
#44
millerh1
opened
2 years ago
1
Discussion points
#43
millerh1
opened
2 years ago
0
Immune cell analysis
#42
millerh1
closed
2 years ago
1
GTEx experiments
#41
millerh1
opened
2 years ago
2
Unit tests for the analysis
#40
millerh1
closed
2 years ago
1
Plot idea -- show the gradient of predictions overtop the PCA plot
#39
millerh1
closed
2 years ago
1
Need to figure out why precision for PLIER is so much higher than autoPLIER in current tests
#38
millerh1
closed
2 years ago
2
Need to remove standard scaling and re-run experiments
#37
millerh1
closed
2 years ago
1
Need to analyze methods for setting the L1 param
#36
millerh1
closed
2 years ago
2
Test relationship between the number of LVs, the number of pathways, and the performance of the classifier
#35
millerh1
closed
2 years ago
1
Test new methods for setting number of LVs
#34
millerh1
closed
2 years ago
1
Sanity check: can we correctly distinguish cell types?
#33
millerh1
closed
2 years ago
1
Autoplier analysis
#32
millerh1
closed
2 years ago
0
Analysis of COVID-19 data
#31
mbernste
closed
2 years ago
0
COVID dataset
#30
millerh1
closed
2 years ago
1
Train the cell type classifiers using autoPLIER -- how does it perform compared to PCA?
#29
millerh1
closed
2 years ago
1
compare autoPLIER to PLIER
#28
millerh1
closed
2 years ago
1
Model tuning
#27
millerh1
closed
2 years ago
7
Experiment: MEF -> iPSCs testing
#26
millerh1
opened
2 years ago
0
Experiment: JDRF data analysis
#25
millerh1
closed
2 years ago
1
Initial maniscript: Distinctions from other methods
#24
millerh1
opened
2 years ago
0
added cello-multiplier module and usage example
#13
Julian-Borbeck
closed
3 years ago
0
EDA_Julian/Ewing-TF-IDF.ipynb
#12
Julian-Borbeck
closed
3 years ago
1
Build a diagram of the final software package
#11
millerh1
closed
3 years ago
0
Put together a long-term roadmap for the project
#8
millerh1
closed
3 years ago
0
Try the linear regression on the training data (leave n out and then can you correctly find the LVs for them?)
#6
millerh1
closed
3 years ago
0
UMAP and clusters -- check the LV levels and then:
#5
millerh1
closed
3 years ago
0
Benchmark classifiers
#4
millerh1
closed
3 years ago
0
Evaluate previous classifiers
#3
millerh1
closed
3 years ago
0
Exploratory data analysis & preprocessing of training dataset
#2
millerh1
closed
3 years ago
0
Generate training data
#1
millerh1
closed
3 years ago
1