From 5f2ea294721ce7ab92b4a24655b8a59af0c2bd4d Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Wed, 24 Jun 2026 14:57:01 -0700
Subject: [PATCH 1/2] Access the `raw` slot when initializing form anndata/h5ad
 objects

---
 CHANGELOG.md                                  |  3 ++-
 .../SingleCellExperiment.py                   | 22 +++++++++++++++----
 tests/test_sce_io.py                          | 10 +++++++++
 3 files changed, 30 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 73b6fb3..8d17b17 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,11 +1,12 @@
 # Changelog
 
-## Version 0.6.0 - 0.6.2
+## Version 0.6.0 - 0.6.3
 
 - Changed related to SummarizedExperiment and implementation of `CompressedGenomicRangesList` in the genomic ranges package.
 - Update versions of relevant dependency packages.
 - Rename `reduced_dims` to `reduced_dimensions`.
 - Implement coercions to/from RSE/SE.
+- Access data stored in `raw` (if available) as `alternative_experiments`, when initializing `SingleCellExperiment` objects from anndata/h5ad files.
 
 ## Version 0.5.8 - 0.5.9
 
diff --git a/src/singlecellexperiment/SingleCellExperiment.py b/src/singlecellexperiment/SingleCellExperiment.py
index e35330a..745e206 100644
--- a/src/singlecellexperiment/SingleCellExperiment.py
+++ b/src/singlecellexperiment/SingleCellExperiment.py
@@ -1195,14 +1195,18 @@ def to_anndata(self, include_alternative_experiments: bool = False):
     def from_anndata(cls, input: "anndata.AnnData") -> SingleCellExperiment:
         """Create a ``SingleCellExperiment`` from :py:class:`~anndata.AnnData`.
 
-         Args:
+        If the input contains any data in the ``uns`` attribute, the
+        `metadata` slot of the ``SingleCellExperiment`` will contain a key ``uns``.
+
+        If the input contains ``raw`` data, the ``SingleCellExperiment``
+        will contain an alternative experiment called ``raw``.
+
+        Args:
             input:
                 Input data.
 
         Returns:
-            A ``SingleCellExperiment`` object. If the input contains any data
-            in the ``uns`` attribute, the `metadata` slot of the ``SingleCellExperiment``
-            will contain a key ``uns``.
+            A ``SingleCellExperiment`` object.
         """
 
         layers = OrderedDict()
@@ -1217,6 +1221,15 @@ def from_anndata(cls, input: "anndata.AnnData") -> SingleCellExperiment:
         obsp = _to_normal_dict(input.obsp)
         _metadata = {"uns": input.uns} if input.uns is not None else None
 
+        alt_expts = None
+        if input.raw is not None:
+            raw_se = SummarizedExperiment(
+                assays={"X": input.raw.X.transpose()},
+                row_data=biocframe.BiocFrame.from_pandas(input.raw.var),
+                column_data=biocframe.BiocFrame.from_pandas(input.obs),
+            )
+            alt_expts = {"raw": raw_se}
+
         return cls(
             assays=layers,
             row_data=biocframe.BiocFrame.from_pandas(input.var),
@@ -1225,6 +1238,7 @@ def from_anndata(cls, input: "anndata.AnnData") -> SingleCellExperiment:
             reduced_dimensions=obsm,
             row_pairs=varp,
             column_pairs=obsp,
+            alternative_experiments=alt_expts,
         )
 
     ###############################
diff --git a/tests/test_sce_io.py b/tests/test_sce_io.py
index e7eba44..0b15379 100644
--- a/tests/test_sce_io.py
+++ b/tests/test_sce_io.py
@@ -198,6 +198,16 @@ def test_SCE_randomAnnData():
     assert tse is not None
     assert isinstance(tse, SingleCellExperiment)
 
+    # set raw
+    adata.raw = adata.copy()
+    tse = singlecellexperiment.SingleCellExperiment.from_anndata(adata)
+
+    assert tse is not None
+    assert isinstance(tse, SingleCellExperiment)
+    assert tse.alternative_experiments is not None
+    assert "raw" in tse.alternative_experiments 
+    assert isinstance(tse.alternative_experiments["raw"], SummarizedExperiment)
+    assert tse.alternative_experiments["raw"].shape == (d, n)
 
 def test_SCE_to_mudata():
     tse = SingleCellExperiment(

From 1914130d613e9885fdea50b3b36e3c7cfccb5c09 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 24 Jun 2026 21:57:32 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_sce_io.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_sce_io.py b/tests/test_sce_io.py
index 0b15379..424b0cd 100644
--- a/tests/test_sce_io.py
+++ b/tests/test_sce_io.py
@@ -205,7 +205,7 @@ def test_SCE_randomAnnData():
     assert tse is not None
     assert isinstance(tse, SingleCellExperiment)
     assert tse.alternative_experiments is not None
-    assert "raw" in tse.alternative_experiments 
+    assert "raw" in tse.alternative_experiments
     assert isinstance(tse.alternative_experiments["raw"], SummarizedExperiment)
     assert tse.alternative_experiments["raw"].shape == (d, n)