Update README.md

README.md

@@ -4,7 +4,14 @@ license: cc-by-4.0
 
 # Chem-PerturBridge
 
-Processed group-replicate `.h5ad` files from Chem-PerturBridge datasets whose upstream terms allow redistribution.
+Processed standardized expression `.h5ad` files and differential gene expression (DGE) `.h5ad` outputs from Chem-PerturBridge datasets whose upstream terms allow redistribution.
+
+This repository contains:
+
+- processed group-replicate bulk or pseudobulk input files under `<dataset>/`
+- DGE outputs under `<dataset>/group_rep/` and `<dataset>/sep_rep/`
+
+The DGE replicate modes indicate whether the DGE analysis was run using all replicates or per replicate (for within-dataset agreement evaluation), shortened to `group_rep` and `sep_rep`.
 
 ## License
 
@@ -12,10 +19,12 @@ The collection curation and packaging are released under CC BY 4.0.
 
 CC BY 4.0 for Chem-PerturBridge curation/packaging; preserve each upstream license, notice, and attribution.
 
-Each upstream dataset retains its original license, attribution, and notice requirements. See `upload_manifest.tsv` for per-dataset provenance.
+Each upstream dataset retains its original license, attribution, and notice requirements. See `upload_manifest.tsv` for processed-file provenance and `dge_upload_manifest.tsv` for per-DGE-file provenance.
 
 ## Files
 
+### Processed Input Files
+
 - `l1000_phase1/`: `l1000_phase1_level3_deg_ready_landmark_processed.h5ad` (NCBI/GEO public data; NCBI places no use/distribution restrictions)
 - `l1000_phase2/`: `l1000_phase2_level3_deg_ready_landmark_processed.h5ad` (NCBI/GEO public data; NCBI places no use/distribution restrictions)
 - `novartis_batch_2500/`: `novartis_standardized_processed.h5ad` (MIT License)
@@ -25,6 +34,57 @@ Each upstream dataset retains its original license, attribution, and notice requ
 - `vcpi_0001/`: `vcpi_0001_standardized_processed.h5ad` (CC BY 4.0 for public VCPI releases)
 - `vcpi_0002/`: `vcpi_0002_standardized_processed.h5ad` (CC BY 4.0 for public VCPI releases)
 
+### Differential Expression Files
+
+DGE files are organized as `<dataset>/<replicate_mode>/<cell_line>_de.h5ad`. Each file contains treatment-vs-control contrasts for one cell line or context.
+
+| Dataset | `group_rep` files | `sep_rep` files | Total DGE files |
+|---|---:|---:|---:|
+| `l1000_phase1` | 70 | 70 | 140 |
+| `l1000_phase2` | 30 | 30 | 60 |
+| `novartis_batch_2500` | 1 | 1 | 2 |
+| `op3` | 4 | 4 | 8 |
+| `sciplex` | 3 | 3 | 6 |
+| `tahoe` | 48 | 48 | 96 |
+| `vcpi_0001` | 1 | 1 | 2 |
+| `vcpi_0002` | 1 | 1 | 2 |
+| **Total** | **158** | **158** | **316** |
+
+## Manifests
+
+- `upload_manifest.tsv`: one row per processed input file, including path, source, upstream license, and required notice.
+- `dge_upload_manifest.tsv`: one row per DGE file, including dataset, replicate mode, cell line/context, repository path, source, upstream license, and required notice.
+
+## AnnData Schema
+
+### Processed Input `.h5ad`
+
+Rows in `.obs` represent standardized bulk samples or pseudobulk profiles. Core metadata fields include `plate`, `well`, `cell_type`, `perturbagen`, `pert_type`, `is_control`, `pert_dose_uM`, `pert_time_h`, `suspension_type`, `tissue`, `tissue_type`, `disease`, `library`, `stimulation`, `guide`, `dataset`, `assay`, `development_stage`, `organism`, `sex`, `self_reported_ethnicity`, `pubchem_cid`, `psbulk_cells`, and `psbulk_counts` where available.
+
+Columns in `.var` represent genes and include `symbol`; some files include additional gene annotations such as merged-gene indicators. `.X` stores the standardized expression matrix. For single-cell-derived pseudobulk files, `.X` contains pseudobulk counts and `.layers["psbulk_props"]` may contain pseudobulk proportions. Bulk-derived datasets may represent raw counts, normalized expression, or platform-specific intensity values depending on the upstream assay and preprocessing.
+
+### DGE `.h5ad`
+
+Rows in `.obs` represent treatment-vs-control contrasts for one cell line or context. The row index is the contrast label, and metadata is inherited from the treated condition after DGE preprocessing.
+
+Columns in `.var` represent genes and carry gene annotations from the processed input file.
+
+`.X` is intentionally absent from DGE files; DGE statistics are stored in `.layers`:
+
+- `logFC`
+- `stdev.unscaled`
+- `stdev.scaled`
+- `CI.L`
+- `CI.R`
+- `AveExpr`
+- `t`
+- `P.Value`
+- `adj.P.Value.within_one_contrast`
+- `adj.P.Value.across_all_contrasts`
+- `B`
+
+`.uns` includes upstream metadata carried from the processed input plus DGE processing metadata such as `threshold_filter_cells` and `qc_filtering_enabled`.
+
 ## Sources And Notices
 
 - `l1000_phase1`: LINCS L1000 Phase I, GEO GSE92742 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92742. Cite LINCS L1000/GSE92742 and preserve upstream attribution.