├── .gitignore ├── LICENSE ├── README.md ├── data ├── A.csv ├── S.csv ├── TRN.csv ├── curated_enrichments.csv ├── gene_info.csv ├── imodulon_gene_bnumbers.txt ├── imodulon_gene_names.txt ├── log_tpm.csv ├── log_tpm_full.csv ├── log_tpm_norm.csv └── metadata.csv ├── environment.yml ├── modulons.pdf ├── notebooks └── exploratory_analysis.ipynb └── scripts ├── cluster_components.py ├── compute_distance.py ├── random_restart_ica.py └── run_ica.sh /.gitignore: -------------------------------------------------------------------------------- 1 | .ipynb_checkpoints 2 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/README.md -------------------------------------------------------------------------------- /data/A.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/data/A.csv -------------------------------------------------------------------------------- /data/S.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/data/S.csv -------------------------------------------------------------------------------- /data/TRN.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/data/TRN.csv -------------------------------------------------------------------------------- /data/curated_enrichments.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/data/curated_enrichments.csv -------------------------------------------------------------------------------- /data/gene_info.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/data/gene_info.csv -------------------------------------------------------------------------------- /data/imodulon_gene_bnumbers.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/data/imodulon_gene_bnumbers.txt -------------------------------------------------------------------------------- /data/imodulon_gene_names.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/data/imodulon_gene_names.txt -------------------------------------------------------------------------------- /data/log_tpm.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/data/log_tpm.csv -------------------------------------------------------------------------------- /data/log_tpm_full.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/data/log_tpm_full.csv -------------------------------------------------------------------------------- /data/log_tpm_norm.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/data/log_tpm_norm.csv -------------------------------------------------------------------------------- /data/metadata.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/data/metadata.csv -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/environment.yml -------------------------------------------------------------------------------- /modulons.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/modulons.pdf -------------------------------------------------------------------------------- /notebooks/exploratory_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/notebooks/exploratory_analysis.ipynb -------------------------------------------------------------------------------- /scripts/cluster_components.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/scripts/cluster_components.py -------------------------------------------------------------------------------- /scripts/compute_distance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/scripts/compute_distance.py -------------------------------------------------------------------------------- /scripts/random_restart_ica.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/scripts/random_restart_ica.py -------------------------------------------------------------------------------- /scripts/run_ica.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBRG/precise-db/HEAD/scripts/run_ica.sh --------------------------------------------------------------------------------