annotate becker dataset

theislab · Dec 20, 2023 · c523570 · c523570
1 parent b672dc4
commit c523570
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Showing 5 changed files with 28 additions and 1 deletion.
diff --git a/...a/dataloaders/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001.py b/...a/dataloaders/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001.py
@@ -9,5 +9,5 @@ def load(data_dir, **kwargs):
     fn = os.path.join(data_dir, "becker_crc.h5ad")
     # replace the simple data loading code below with the code required to load your data file(s)
     adata = anndata.read_h5ad(fn)
-
+    adata.obs["age"] = adata.obs["age"].astype(str)
     return adata  # your load function needs to return an AnnData object
diff --git a/...rs/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001_development_stage.tsv b/...rs/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001_development_stage.tsv
@@ -0,0 +1,13 @@
+source	target	target_id
+20	20-year-old human stage	HsapDv:0000114
+22	22-year-old human stage	HsapDv:0000116
+31	31-year-old human stage	HsapDv:0000125
+35	35-year-old human stage	HsapDv:0000129
+47	47-year-old human stage	HsapDv:0000141
+53	53-year-old human stage	HsapDv:0000147
+55	55-year-old human stage	HsapDv:0000149
+58	58-year-old human stage	HsapDv:0000152
+61	61-year-old human stage	HsapDv:0000155
+66	66-year-old human stage	HsapDv:0000160
+67	67-year-old human stage	HsapDv:0000161
+78	78-year-old human stage	HsapDv:0000172
diff --git a/...ders/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001_disease.tsv b/...ders/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001_disease.tsv
@@ -0,0 +1,4 @@
+source	target	target_id
+FAP	classic familial adenomatous polyposis	MONDO:0021055
+Healthy	healthy	PATO:0000461
+Sporadic CRC	colorectal cancer	MONDO:0005575
diff --git a/...rs/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001_ethnicity.tsv b/...rs/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001_ethnicity.tsv
@@ -0,0 +1,7 @@
+source	target	target_id
+Asian	Asian	HANCESTRO:0008
+Black	African	HANCESTRO:0010
+Hispanic/Latino	Hispanic or Latin American	HANCESTRO:0014
+Other	uncategorised population	HANCESTRO:0018
+White	European	HANCESTRO:0005
+White/Asian	Asian	HANCESTRO:0008
diff --git a/...aloaders/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001_sex.tsv b/...aloaders/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001_sex.tsv
@@ -0,0 +1,3 @@
+source	target	target_id
+F	female	PATO:0000383
+M	male	PATO:0000384