scatrans 0.9.1.dev0__tar.gz → 0.9.2.dev0__tar.gz

scatrans-0.9.2.dev0/LICENSE

@@ -0,0 +1,201 @@
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{scatrans-0.9.1.dev0 → scatrans-0.9.2.dev0}/PKG-INFO

@@ -1,14 +1,14 @@
 Metadata-Version: 2.4
 Name: scatrans
-Version: 0.9.1.dev0
+Version: 0.9.2.dev0
 Summary: Single-cell Active Transcription Analysis
 Author: scATrans Developers
-License: MIT
+License: Apache-2.0
 Project-URL: Homepage, https://github.com/scATrans/scatrans
 Keywords: single-cell,RNA-seq,unspliced,nascent RNA,active transcription,bioinformatics
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
+Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.8
@@ -46,9 +46,9 @@ Dynamic: license-file
 
 # scATrans
 
-scATrans computes a composite score from differential expression and reference-based excess unspliced (nascent) RNA between groups. It ranks genes in single-cell spliced/unspliced or mature/nascent data.
+scATrans is a Python toolkit for single-cell differential analysis. It is primarily designed for datasets that contain spliced/unspliced (or mature/nascent) RNA layers. In this setting it computes a composite active transcription score that integrates differential expression with reference-based excess unspliced RNA to rank genes.
 
-Results must be interpreted using the provided diagnostics. The method has known limitations and does not guarantee recovery of truly active genes.
+Even without spliced/unspliced layers, scATrans remains a complete, self-contained single-cell differential analysis package. It provides multiple differential expression methods (scanpy, PyDESeq2 pseudobulk, linear mixed models, and optional Memento), comprehensive functional enrichment (ORA, GSEA, GO, KEGG with bundled up-to-date gene sets and proper universe handling), and a full suite of publication-ready visualization tools. At present there is no closely comparable all-in-one Python package offering this breadth for single-cell data.
 
 ## Installation
 
@@ -66,7 +66,7 @@ pip install "scatrans[pseudobulk]"
 pip install "scatrans[memento]"
 ```
 
-The package ships precomputed gene feature tables (gene length and intron number) for mouse. These are used for bias correction when available.
+The package ships precomputed gene feature tables (gene length + intron number) for both mouse and human. These are used for optional bias correction in `active_score`. You can also supply custom tables (e.g. from your own GTF).
 
 To install from source:
 
@@ -76,6 +76,30 @@ cd scatrans
 pip install -e ".[dev]"
 ```
 
+**Note on version when installing from git:**
+
+The package uses `setuptools_scm` to determine the version from git tags. If you see `0.8.0.devN` after `pip install @git+...`, it means the repository you are installing from has its latest tag at 0.8.x.
+
+To get version 0.9.0:
+
+- Tag the repository first (recommended):
+  ```bash
+  git tag 0.9.0
+  git push origin 0.9.0
+  ```
+  Then reinstall.
+
+- Or force it for this install:
+  ```bash
+  SETUPTOOLS_SCM_PRETEND_VERSION=0.9.0 pip install -U "scatrans[memento]@git+https://..."
+  ```
+
+After install, verify with:
+```python
+import scatrans as scat
+print(scat.__version__)  # should be 0.9.0
+```
+
 **Logging.** The package logs under the name `scatrans`. You can control verbosity with:
 
 ```python
@@ -254,6 +278,29 @@ enrich_res = scat.run_enrichment(
 #   - res.attrs["universe_info"] with effective_universe_size, dropped_by_annotation_filter, etc.
 ```
 
+**run_gsea** (pre-ranked GSEA for ranked gene lists):
+
+```python
+# ranked list from active_score / differential_expression results
+ranked = all_results["logFC"].sort_values(ascending=False)
+
+gsea_res = scat.run_gsea(
+    ranked_genes=ranked,
+    gene_sets="GO_Biological_Process",
+    organism="mouse",
+    nperm=1000,
+)
+print(gsea_res.head())
+
+scat.pl.enrich_dotplot(gsea_res, x="NES", color_by="NES")
+
+# gseaplot (uses the exact curve stored by run_gsea)
+term = gsea_res.iloc[0]["Term"]
+scat.pl.gseaplot(ranked, gsea_res, term=term)
+```
+
+Requires `pip install "scatrans[gsea]"`.
+
 **run_kegg** (convenience wrapper for KEGG pathways):
 
 ```python
@@ -473,10 +520,6 @@ A dictionary containing:
 
 `diagnose_design` is automatically called inside `active_score(...)` whenever you pass `sample_col` or set `use_pseudobulk=True`. You will see its output in the log.
 
-### run_kegg and simplify_enrichment
-
-These are convenience functions built on top of `run_enrichment`.
-
 **run_kegg** – Run KEGG pathway enrichment directly:
 
 ```python
@@ -495,11 +538,12 @@ kegg_res = scat.run_kegg(
 
 ### run_gsea (pre-ranked GSEA)
 
-For ranked-list enrichment (the classic GSEA approach):
+For ranked-list enrichment (the classic GSEA / prerank approach):
 
 ```python
-# ranked list: higher = more associated with target (e.g. logFC or custom score)
-ranked = all_results.set_index("gene")["logFC"]   # or "active_score" etc.
+# Obtain a ranked gene list (e.g. from active_score or differential_expression results).
+# Convention: higher value = more associated with the target group.
+ranked = all_results["logFC"].sort_values(ascending=False)
 
 gsea_res = scat.run_gsea(
     ranked_genes=ranked,
@@ -507,23 +551,24 @@ gsea_res = scat.run_gsea(
     organism="mouse",
     nperm=1000,
     min_size=15,
-    # gsea_res is a DataFrame with NES, ES, pvalue, p.adjust, leading_edge, ...
 )
-print(gsea_res.head())
-scat.pl.enrich_dotplot(gsea_res, x="NES", color_by="NES")  # auto-friendly
+print(gsea_res[["Term", "NES", "p.adjust", "leading_edge"]].head())
+
+# Works with existing plotting helpers (auto-detects GSEA columns)
+scat.pl.enrich_dotplot(gsea_res, x="NES", color_by="NES")
+
+# Dedicated running-sum plot (uses curves stored by run_gsea)
 scat.pl.gseaplot(ranked, gsea_res, term=gsea_res.iloc[0]["Term"])
 ```
 
-`run_gsea` stores pre-computed RES curves in `.attrs["gsea_details"]` so `gseaplot` can render the exact running sum used for the NES/p-values.
+`run_gsea` stores the full enrichment score curves in `.attrs["gsea_details"]` so that `gseaplot` renders exactly the same RES that produced the reported NES/p-values.
 
-Requires `pip install "scatrans[gsea]"` (or gseapy).
-
-print(kegg_res[["Term", "p.adjust", "Count"]].head())
+Requires the optional extra:
+```bash
+pip install "scatrans[gsea]"   # pulls in gseapy
 ```
 
-The `gene_set_source` parameter (default `"scatrans"`) controls which KEGG set is used.
-See the section "Choosing gene sets explicitly with `gene_set_source`" above for full details
-and examples for both GO and KEGG.
+See the Plotting section below for details on GSEA-aware `enrich_dotplot` and the new `gseaplot`.
 
 **simplify_enrichment** – Remove redundant terms from enrichment results:
 
@@ -701,16 +746,6 @@ Recommended only when you have a reasonable number of cells and want noise reduc
 
 ---
 
-## Limitations
-
-The unspliced excess term is a group-contrast proxy derived from a reference-group gamma calculation. It is not a full stochastic or dynamical model.
-
-Interpretation is simplest for clear binary contrasts. Within-group heterogeneity reduces observed signal. The permutation approximation (used when `use_permutation=True`) fixes unspliced/spliced layers and the reference gamma on the original labels; the note is recorded in the results. Global unspliced fractions above ~50% are flagged as potential technical artifacts. Bias-correction quality depends on the number of genes with length and intron annotations. With few biological replicates, power for the unspliced excess term and permutation-based FDR is limited. Mixed-model statistics tend to be conservative when between-sample variation is large.
-
-Always examine diagnostics, score distributions, and (when available) the original spliced/unspliced counts before biological interpretation.
-
----
-
 ## API Reference (Simplified)
 
 ### Core functions
@@ -718,6 +753,7 @@ Always examine diagnostics, score distributions, and (when available) the origin
 - `active_score(...)` — main analysis for active transcription from velocity data. Returns `(adata_res, significant, all_results)`.
 - `differential_expression(...)` — standalone DE (no velocity data required). Supports the same backends as `active_score` (including optional Memento). Returns `(adata, results_df)`.
 - `filter_active_genes(results_df, ...)` — post-filter the full ranked table. Supports `preset="heuristic" | "pseudobulk" | "permissive"`. Works for both `active_score` and `differential_expression` results.
+- `store_raw_counts` / `ensure_raw_counts` / `restore_raw_counts` — preserve the original full count matrix and spliced/unspliced layers (call early, before HVG/normalize). Essential for correct backgrounds in enrichment and for count-based DE backends.
 
 ### Basic parameters (most users only need these)
 
@@ -747,12 +783,17 @@ Full signatures and all parameters are documented in the function docstrings and
 
 ### Other commonly used functions
 
-- `add_gene_features(adata, organism="mouse", ...)` — attach length/intron info
-- `list_available_gene_features()`
+- `add_gene_features(adata, organism="mouse" or "human", ...)` — attach length/intron info from bundled or custom table
+- `generate_gene_features_from_gtf(gtf_path, output_name, ...)` — build a custom table from a GTF (requires `[gene_features]`)
+- `list_available_gene_features()` — list bundled tables
+- `generate-gene-features` (CLI) — same as above, for the shell
+- `store_raw_counts(adata, layer="counts", save_raw=False)`, `ensure_raw_counts(adata)`, `restore_raw_counts(adata, ...)` — preserve full raw counts + original spliced/unspliced layers before HVG/normalization (critical for correct DE, enrichment background, and Memento/PyDESeq2)
 - `diagnose_design(adata, groupby, target_group, reference_group, sample_col=None)` — analyzes cell/sample counts and global unspliced fraction; returns warnings, recommendations, and a suggested `filter_active_genes` preset. Automatically called internally when `sample_col` or `use_pseudobulk=True` is used.
 - `run_enrichment(...)`, `run_kegg(...)`, `run_go(...)`, `run_gsea(...)`, `simplify_enrichment(...)`, `save_enrichment_report(...)`, `expand_enrichment_genes(...)`, `list_bundled_gene_sets()`
-- `scat.pl.*` plotting functions (comet_plot, volcano_plot, bias_diagnostic_plot, ...)
+- `scat.pl.*` plotting functions (comet_plot, volcano_plot, bias_diagnostic_plot, enrich_dotplot, gseaplot, active_score_rankplot, active_genes_heatmap, velocity_phase_portraits, ...)
 - `scat.qc.unspliced_global(adata)`
+- `scat.pl.set_style()` / `scat.pl.style_context()` — publication-friendly matplotlib style (opt-in, off by default per-plot via use_style=)
+- Submodules `scat.pl` and `scat.qc` (scanpy-style)
 
 ### Layer names
 
@@ -762,13 +803,69 @@ The package auto-detects `mature`/`nascent` (kb_python) and remaps them internal
 
 ## Gene Feature Attachment & CLI
 
+Gene length and intron count are used for optional bias correction inside `active_score`.
+
 ```python
-adata = scat.add_gene_features(adata, organism="mouse")
+# Use bundled tables
+adata = scat.add_gene_features(adata, organism="mouse")   # or organism="human"
+
 # or provide your own table
 adata = scat.add_gene_features(adata, gene_features_path="my_features.parquet")
 ```
 
-After installing the `gene_features` extra, the `generate-gene-features` CLI is available for creating custom tables from GTF files.
+The package ships mouse tables + a human table (`human_GRCh38_2024A_gene_features.parquet`). Use `organism="human"` to select the bundled human table automatically. For other custom annotations, generate your own table and point to it with `gene_features_path`.
+
+### Generating a custom table from GTF
+
+Install the generator:
+
+```bash
+pip install "scatrans[gene_features]"
+```
+
+Use the CLI (works with 10x `genes.gtf` or GENCODE GTFs):
+
+```bash
+# Mouse
+generate-gene-features --gtf /path/to/genes.gtf \
+                       --output my_mouse_features.parquet \
+                       --organism mouse
+
+# Human (GENCODE or 10x)
+generate-gene-features --gtf gencode.v49.primary_assembly.annotation.gtf \
+                       --output human_GRCh38_2024A_gene_features.parquet \
+                       --organism human
+```
+
+Then use it:
+
+```python
+import scatrans as scat
+
+adata = scat.add_gene_features(
+    adata,
+    gene_features_path="human_GRCh38_2024A_gene_features.parquet"
+)
+
+# bias correction will now be able to use length + intron_number
+adata_res, significant, all_results = scat.active_score(adata, ...)
+```
+
+You can also call the generator programmatically:
+
+```python
+from scatrans import generate_gene_features_from_gtf
+
+df = generate_gene_features_from_gtf(
+    "path/to/genes.gtf",
+    output_name="my_custom_features.parquet",
+    organism="human"
+)
+```
+
+See also `scat.list_available_gene_features()` (for bundled tables) and the full signature of `add_gene_features`.
+
+**Tip**: The generated parquet must contain a `gene_name` column (plus `gene_length` and `intron_number`). `add_gene_features` does a `reindex` on your `adata.var_names`.
 
 ---
 
@@ -837,7 +934,14 @@ Most return `(fig, ax)` (or `(fig, axes_list)` for grids like phase portraits) f
 
 ## Command-Line Interface
 
-Only the gene-feature generator is exposed as a CLI (`generate-gene-features`).
+The only console script is the gene-feature table generator:
+
+```bash
+pip install "scatrans[gene_features]"
+generate-gene-features --gtf /path/to/genes.gtf --output my_features.parquet --organism human
+```
+
+See the "Gene Feature Attachment & CLI" section for full examples (mouse/human + how to use the output with `add_gene_features`).
 
 ---
 
@@ -915,9 +1019,21 @@ adata, de_res = scat.differential_expression(adata, use_memento_de=True, ...)
 
 ---
 
+## Limitations
+
+The unspliced excess term (used by the primary `active_score` workflow) is a group-contrast proxy derived from a reference-group gamma calculation. It is not a full stochastic or dynamical model.
+
+Interpretation is simplest for clear binary contrasts. Within-group heterogeneity reduces observed signal. The permutation approximation (used when `use_permutation=True`) fixes unspliced/spliced layers and the reference gamma on the original labels; the note is recorded in the results. Global unspliced fractions above ~50% are flagged as potential technical artifacts. Bias-correction quality depends on the number of genes with length and intron annotations. With few biological replicates, power for the unspliced excess term and permutation-based FDR is limited. Mixed-model statistics tend to be conservative when between-sample variation is large.
+
+When used purely as a differential expression + enrichment toolkit (via `differential_expression`, `run_enrichment`, etc.), scATrans relies on established backends (scanpy, PyDESeq2, etc.) whose standard statistical caveats apply.
+
+Always examine diagnostics, score distributions, and (when available) the original spliced/unspliced counts before biological interpretation.
+
+---
+
 ## License
 
-MIT License.
+Apache License 2.0.
 
 ---