zrcjessica / cts_cnn

Chromatin Accessibility Prediction for ATAC-Seq Data with CNN

Required Packages

Numpy, PyTorch, Sklearn, Scipy, random, seaborn, matplotlib, Math, os

Binary Classification

Individual Cell Type

Prediction for each cell type spearately

Data

Processed count data w/ 0~50 cut

/iblm/netapp/home/sherryh/rats/50cut

Or generated from

/iblm/netapp/home/jezhou/make_cnn_training_data/out/pseudobulk

Training/Testing

single_cell_binary.ipynb

Note:
Ignore Data Encoding Type 1 and Trainer for Continuous Data and run all other cells.
There are six available models, but using CNN Naive Model would be sufficient.

Jointly for Eight Cell Type

Prediction for cell types together, including Endothelial, Astrocytes, OPC, InhNeuron, ExNeuron, Microglia, Oligodendrocytes, Sst+.

Data

Merged count data w/ 25~50cut

/iblm/netapp/home/sherryh/binary_data/50cut

/iblm/netapp/home/sherryh/binary_data/25cut

Generated from MACS2

/iblm/netapp/home/sherryh/binary_data/MACS2

Training/Testing

Multi_cell.ipynb

Note:
Run all cells and select model of choice, CNN works the best.

Quantitative Prediction

Individual Cell Type

Prediction for each cell type spearately

Data

Processed count data

/iblm/netapp/home/sherryh/new_data/zscore/

/iblm/netapp/home/sherryh/new_data/zscore_125/

/iblm/netapp/home/sherryh/new_data/zscore_500/

Or generated from

/iblm/netapp/home/jezhou/make_cnn_training_data/out/pseudobulk

Training/Testing

single_cell_continuous.ipynb

Note:
There are seven available models, but only CNN is constructed to handle different datasets. Need to manually change feed forward layer size for other models.

Jointly for Eight Cell Type

Prediction for cell types together, including Endothelial, Astrocytes, OPC, InhNeuron, ExNeuron, Microglia, Oligodendrocytes, Sst+.

Data

/iblm/netapp/home/sherryh/new_data/zscore/merged_80000_rand.npz

Training/Testing

multi_quant.ipynb

Note:
Not recommend for quantitative prediction as it yields much worse results than training inidividually

Expression Prediction

Individual Cell Type

Prediction for each cell type spearately

Data

Single Cell Data

/iblm/netapp/home/sherryh/expression/full_dataset GTEX data /iblm/netapp/home/sherryh/expression/gtex