zip file content:

- supirfactor-biorxiv-v1.zip: Software package of supirfactor implementation for
                              results reproduction,
                              for latest version see: https://gitlab.com/Xparx/supirfactor.

- encode_prior: Contains the encode generated PBMC prior.
  - ENCODE_ACCESSION_SUPPLEMENTAL_DATA.tsv.gz Datasets used
  - PBMC_50kup_2kdown_TF_ChIP_thresholded.tsv.gz Prior matrix
- pbmc_model: Contains the PBMC model.
- pbmc_results: Contains the metrics, gene enrichments, TFA and meta TFA estimates
                for both the training data and the covid dataset.
  - pbmc
    - Context_metrics_sparse.tsv.gz Performance metric per celltype
    - Gene_Enrichment_metaTFs.tsv   Enrichment analysis for metaTFs.
    - GRN_sparse_indirect.tsv.gz    PBMC GRN
    - GRN_sparse_prior.tsv.gz       PBMC used model prior
    - GRN_sparse.tsv.gz             metaTF to gene regulatory connections. 
    - MTFA_sparse.h5ad              metaTF activity dataset
    - TFA_sparse.h5ad               TF activity dataset
  - covid_pbmc
    - healthy_covid_TFA.h5ad TF activity for covid data.

- yeast_model: Contains the full and sparse version of the yeast hierarchical model
  - model_full_alt.pt   Full yeast model
  - model_sparse_alt.pt Sparse yeast model

- yeast_results: Contains the performance metrics, gene enrichments,
                 TFA and meta TFA estimates for yeast results.
  - Context_metrics_sparse_alt.tsv.gz Context specific performance metrics.
  - Gene_Enrichment_metaTFs.tsv       Enrichment analysis of meta TF targets.
  - GRN_sparse_alt_indirect.tsv.gz    GRN TF to gene network.
  - GRN_sparse_alt_prior.tsv.gz       Used model prior.
  - GRN_sparse_alt.tsv.gz             GRN metaTF to gene network.
  - MTFA_sparse_alt.h5ad              meta TF activity dataset 
  - TFA_sparse_alt.h5ad               TF activity dataset.

Transcription Factor (TF).