ONION_git

Code repository for preprint 'Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens'

DOI: https://doi.org/10.1101/2023.02.22.529573

Repository for autoencoder-normalization code: https://github.com/csbio/ae-norm

Repository for input data and output files : https://zenodo.org/record/7671685#.Y_gi9nbMK5c

Directory Set Up

-Download ONION-git repo.

-All source codes (R scripts) are in the ONION-git/src directory.

-Create 'data' directory in ONION-git.

-Input data required for this are uploaded here - https://zenodo.org/record/7671685#.Y_gi9nbMK5c

-Create 'output' directory in ONION-git. Create 'ae','pca','rpca' and 'onion' directories in the 'output' directory.

-Download FLEX and put in the same directory as the ONION-git.

-Required directory and file organization

.
 ├── ONION-git
 │   ├── src                     
 │   │   ├── ...                                                    # provided R scripts
 │   ├── data
 │   │   ├── 20Q2_GLS_fdr.npy                                       
 │   │   ├── 20Q2_GLS_sign.npy
 │   │   ├── Achilles_gene_effect.csv
 │   │   ├── depmap_q2_2020_nona_mean.tsv
 │   │   ├── depmap_q2_2020_nona_mean_rst_clp_mms.tsv
 │   │   ├── all_genes_20q2.txt
 │   │   ├── Mitochondial_genelist_1_26_2021_genes.tsv
 │   │   ├── olfactory_receptors.csv
 │   │   ├── ae_tanh_e1_depmap_20q2
 │   │   │   ├── 20q2_epochs_1_latent_1_normalized_ae.tsv
 │   │   │   ├── 20q2_epochs_1_latent_2_normalized_ae.tsv
 │   │   │   ├── 20q2_epochs_1_latent_3_normalized_ae.tsv
 │   │   │   ├── 20q2_epochs_1_latent_4_normalized_ae.tsv
 │   │   │   ├── 20q2_epochs_1_latent_5_normalized_ae.tsv
 │   │   │   ├── 20q2_epochs_1_latent_10_normalized_ae.tsv
 │   ├── output
 │   │   ├── ae
 │   │   │   ├── ...                                              # outputs are created after running R scripts
 │   │   ├── pca
 │   │   │   ├── ...                                              # outputs are created after running R scripts
 │   │   ├── rpca
 │   │   │   ├── ...                                              # outputs are created after running R scripts
 │   │   ├── onion
 │   │   │   ├── ...                                              # outputs are created after running R scripts
 ├── FLEX
 │   ├── ...                                                      # Directories from FLEX package

Run instruction

-Required packages and dependencies should be installed prior to running the scripts. Required packages are listed in the 'R packages'.

-Run from inside src directory in the given order. Some scripts are dependent on outputs from other scripts. Please refer to script_dependency_flow_.pdf for script dependency.

-Please refer to data_flow_.pdf and data_flow_2_.pdf for script input/output flow.

 Rscript pre_process.R
 Rscript pca_normalization_pipeline.R
 Rscript rpca_normalization_pipeline.R
 Rscript ae_normalization_pipeline.R
 Rscript network_correlation_pipeline.R
 Rscript pca_onion_pipeline.R
 Rscript rpca_onion_pipeline.R
 Rscript ae_onion_pipeline.R
 Rscript pre_process_gls.R
 Rscript onion_evaluation_pipeline.R
 Rscript AUPRC_barplot_layer_evaluation_pipeline.R
 Rscript AUPRC_barplot_onion_evaluation_pipeline.R

Script list

Pre-process DepMap data:

pre_process.R

PCA-normalization:

pca_normalization_pipeline.R

RPCA-normalization:

rpca_normalization_pipeline.R

AE-normalization:

ae_normalization_pipeline.R

PC-Onion:

pca_onion_pipeline.R

RPC-Onion:

rpca_onion_pipeline.R

AE-Onion:

ae_onion_pipeline.R

Evaluation:

network_correlation_pipeline.R

pre_process_gls.R

onion_evaluation_pipeline.R

AUPRC_barplot_layer_evaluation_pipeline.R

AUPRC_barplot_onion_evaluation_pipeline.R