pertpy 0.6.0__py3-none-any.whl → 0.8.0__py3-none-any.whl

pertpy/data/_datasets.py

@@ -40,7 +40,7 @@ def papalexi_2021() -> MuData:  # pragma: no cover
     import muon as mu
 
     output_file_name = "papalexi_2021.h5mu"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/36509460",
@@ -63,7 +63,7 @@ def sc_sim_augur() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of a simulated single-cell RNA seq dataset
     """
     output_file_name = "sc_sim_augur.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/31645886",
@@ -93,7 +93,7 @@ def bhattacherjee() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of a single-cell RNA seq dataset
     """
     output_file_name = "bhattacherjee_rna.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/34526528",
@@ -110,9 +110,7 @@ def sciplex3_raw() -> AnnData:  # pragma: no cover
     """Raw sciplex3 perturbation dataset curated for perturbation modeling.
 
     References:
-        Srivatsan SR, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J,
-        Pliner HA, Jackson DL, Daza RM, Christiansen L, Zhang F, Steemers F,
-        Shendure J, Trapnell C. Massively multiplex chemical transcriptomics at
+        Srivatsan SR et al., Trapnell C. Massively multiplex chemical transcriptomics at
         single-cell resolution. Science. 2020 Jan 3;367(6473):45-51.
         doi: 10.1126/science.aax6234. Epub 2019 Dec 5. PMID: 31806696; PMCID: PMC7289078.
 
@@ -120,7 +118,7 @@ def sciplex3_raw() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of a single-cell RNA seq dataset
     """
     output_file_name = "sciplex3.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/33979517",
@@ -133,8 +131,12 @@ def sciplex3_raw() -> AnnData:  # pragma: no cover
     return adata
 
 
-def smillie() -> AnnData:  # pragma: no cover
-    """scRNA-seq data of the small intestine of mice under Ulcerative Colitis.
+def tasccoda_example() -> AnnData:  # pragma: no cover
+    """Example for the coda part of a mudata object.
+
+    Resulting AnnData object (mudata['coda']) when preparing a dataset for processing with tascCODA.
+    Created using the smillie dataset, which comprises scRNA-seq data of the small intestine of mice under Ulcerative Colitis.
+    The full dataset containing the actual count data can be obtained via smillie_2019().
 
     References:
         Smillie, Christopher S et al. “Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.”
@@ -143,8 +145,8 @@ def smillie() -> AnnData:  # pragma: no cover
     Returns:
         :class:`~anndata.AnnData` object of the dataset.
     """
-    output_file_name = "smillie.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_name = "tasccoda_smillie.h5ad"
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/38648585",
@@ -173,7 +175,7 @@ def frangieh_2021() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of the Perturb-CITE-seq data.
     """
     output_file_name = "frangieh_2021.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/34013717",
@@ -202,7 +204,7 @@ def frangieh_2021_raw() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of raw Perturb-CITE-seq data.
     """
     output_file_name = "frangieh_2021_raw.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/34012565",
@@ -231,7 +233,7 @@ def dixit_2016_raw() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of raw Perturb-seq data.
     """
     output_file_name = "dixit_2016_raw.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/34012565",
@@ -260,7 +262,7 @@ def dixit_2016() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of Perturb-seq data
     """
     output_file_name = "dixit_2016.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/34014608",
@@ -288,7 +290,7 @@ def norman_2019() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of single-cell pooled CRISPR screening.
     """
     output_file_name = "norman_2019.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/34027562",
@@ -316,7 +318,7 @@ def norman_2019_raw() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of raw single-cell pooled CRISPR screening
     """
     output_file_name = "norman_2019_raw.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/34002548",
@@ -339,10 +341,10 @@ def dialogue_example() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object
     """
     output_file_name = "dialogue_example.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://figshare.com/ndownloader/files/34490714",
+            url="https://figshare.com/ndownloader/files/43462662",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -361,7 +363,7 @@ def distance_example() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object
     """
     output_file_name = "distances_example_data.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/39561379",
@@ -392,7 +394,7 @@ def kang_2018() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of droplet-based single cell RNA-sequencing
     """
     output_file_name = "kang_2018.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/34464122",
@@ -421,7 +423,7 @@ def stephenson_2021_subsampled() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scRNA-seq profiles
     """
     output_file_name = "stephenson_2021_subsampled.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/38171703",
@@ -448,7 +450,7 @@ def haber_2017_regions() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object
     """
     output_file_name = "haber_2017_regions.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/38169900",
@@ -475,10 +477,10 @@ def adamson_2016_pilot() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "adamson_2016_pilot.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/AdamsonWeissman2016_GSM2406675_10X001.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/AdamsonWeissman2016_GSM2406675_10X001.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -506,10 +508,10 @@ def adamson_2016_upr_epistasis() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb preparedsingle-cell perturbation data
     """
     output_file_name = "adamson_2016_upr_epistasis.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/AdamsonWeissman2016_GSM2406677_10X005.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/AdamsonWeissman2016_GSM2406677_10X005.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -535,10 +537,10 @@ def adamson_2016_upr_perturb_seq() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "adamson_2016_upr_perturb_seq.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/AdamsonWeissman2016_GSM2406681_10X010.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/AdamsonWeissman2016_GSM2406681_10X010.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -562,10 +564,10 @@ def aissa_2021() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb single-cell perturbation data
     """
     output_file_name = "aissa_2021.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/AissaBenevolenskaya2021.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/AissaBenevolenskaya2021.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -591,10 +593,10 @@ def chang_2021() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "chang_2021.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/ChangYe2021.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/ChangYe2021.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -622,10 +624,10 @@ def datlinger_2017() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "datlinger_2017.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/DatlingerBock2017.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/DatlingerBock2017.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -652,10 +654,10 @@ def datlinger_2021() -> AnnData:  # pragma: no cover
          :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "datlinger_2021.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/DatlingerBock2021.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/DatlingerBock2021.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -683,10 +685,10 @@ def frangieh_2021_protein() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "frangieh_2021_protein.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/FrangiehIzar2021_protein.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/FrangiehIzar2021_protein.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -714,10 +716,10 @@ def frangieh_2021_rna() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "frangieh_2021_rna.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/FrangiehIzar2021_RNA.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/FrangiehIzar2021_RNA.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -742,10 +744,10 @@ def gasperini_2019_atscale() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "gasperini_2019_atscale.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/GasperiniShendure2019_atscale.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/GasperiniShendure2019_atscale.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -771,10 +773,10 @@ def gasperini_2019_highmoi() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb single-cell perturbation data
     """
     output_file_name = "gasperini_2019_highmoi.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/GasperiniShendure2019_highMOI.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/GasperiniShendure2019_highMOI.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -800,10 +802,10 @@ def gasperini_2019_lowmoi() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "gasperini_2019_lowmoi.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/GasperiniShendure2019_lowMOI.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/GasperiniShendure2019_lowMOI.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -828,10 +830,10 @@ def gehring_2019() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of a scPerturb prepared single-cell dataset
     """
     output_file_name = "gehring_2019.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/GehringPachter2019.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/GehringPachter2019.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -857,10 +859,10 @@ def mcfarland_2020() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb single-cell perturbation data
     """
     output_file_name = "mcfarland_2020.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/McFarlandTsherniak2020.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/McFarlandTsherniak2020.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -886,10 +888,10 @@ def replogle_2022_k562_essential() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "replogle_2022_k562_essential.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/ReplogleWeissman2022_K562_essential.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/ReplogleWeissman2022_K562_essential.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -900,7 +902,7 @@ def replogle_2022_k562_essential() -> AnnData:  # pragma: no cover
 
 
 def replogle_2022_k562_gwps() -> AnnData:  # pragma: no cover
-    """K562 cells transduced with CRISPRi (day 8 after transcduction).
+    """K562 cells transduced with CRISPRi (day 8 after transduction).
 
     Here, the authors used a compact, multiplexed CRISPR interference (CRISPRi) library
     to assay thousands of loss-of-function genetic perturbations with single-cell RNA sequencing
@@ -917,10 +919,10 @@ def replogle_2022_k562_gwps() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "replogle_2022_k562_gwps.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/ReplogleWeissman2022_K562_gwps.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/ReplogleWeissman2022_K562_gwps.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -931,7 +933,7 @@ def replogle_2022_k562_gwps() -> AnnData:  # pragma: no cover
 
 
 def replogle_2022_rpe1() -> AnnData:  # pragma: no cover
-    """RPE1 cells transduced with CRISPRi (day 7 after transcduction).
+    """RPE1 cells transduced with CRISPRi (day 7 after transduction).
 
     For day 7 essential-scale Perturb-seq experiment in retinal pigment epithelial (RPE1)
     cell lines, library lentivirus was packaged into lentivirus in 293T cells and
@@ -947,10 +949,10 @@ def replogle_2022_rpe1() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "replogle_2022_rpe1.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/ReplogleWeissman2022_rpe1.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/ReplogleWeissman2022_rpe1.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -978,10 +980,10 @@ def schiebinger_2019_16day() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb single-cell perturbation data
     """
     output_file_name = "schiebinger_2019_16day.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/SchiebingerLander2019_GSE106340.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/SchiebingerLander2019_GSE106340.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1007,10 +1009,10 @@ def schiebinger_2019_18day() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb single-cell perturbation data
     """
     output_file_name = "Schiebinger_2019_18day.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/SchiebingerLander2019_GSE115943.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/SchiebingerLander2019_GSE115943.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1036,10 +1038,10 @@ def schraivogel_2020_tap_screen_chr11() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb single-cell perturbation data
     """
     output_file_name = "schraivogel_2020_tap_screen_chr11.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/SchraivogelSteinmetz2020_TAP_SCREEN__chromosome_11_screen.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/SchraivogelSteinmetz2020_TAP_SCREEN__chromosome_11_screen.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1065,10 +1067,10 @@ def schraivogel_2020_tap_screen_chr8() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "schraivogel_2020_tap_screen_chr8.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/SchraivogelSteinmetz2020_TAP_SCREEN__chromosome_8_screen.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/SchraivogelSteinmetz2020_TAP_SCREEN__chromosome_8_screen.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1095,10 +1097,10 @@ def shifrut_2018() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "shifrut_2018.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/ShifrutMarson2018.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/ShifrutMarson2018.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1126,10 +1128,10 @@ def srivatsan_2020_sciplex2() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "srivatsan_2020_sciplex2.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/SrivatsanTrapnell2020_sciplex2.h5ad?download=1",
+            url="https://zenodo.org/record/10044268/files/SrivatsanTrapnell2020_sciplex2.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1155,10 +1157,10 @@ def srivatsan_2020_sciplex3() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "srivatsan_2020_sciplex3.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/SrivatsanTrapnell2020_sciplex3.h5ad?download=1",
+            url="https://zenodo.org/records/10044268/files/SrivatsanTrapnell2020_sciplex3.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1187,10 +1189,10 @@ def srivatsan_2020_sciplex4() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "srivatsan_2020_sciplex4.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/SrivatsanTrapnell2020_sciplex4.h5ad?download=1",
+            url="https://zenodo.org/records/10044268/files/SrivatsanTrapnell2020_sciplex4.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1219,10 +1221,10 @@ def tian_2019_day7neuron() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "tian_2019_day7neuron.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/TianKampmann2019_day7neuron.h5ad?download=1",
+            url="https://zenodo.org/records/10044268/files/TianKampmann2019_day7neuron.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1251,10 +1253,10 @@ def tian_2019_ipsc() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "tian_2019_iPSC.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/TianKampmann2019_iPSC.h5ad?download=1",
+            url="https://zenodo.org/records/10044268/files/TianKampmann2019_iPSC.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1281,10 +1283,10 @@ def tian_2021_crispra() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb single-cell perturbation data
     """
     output_file_name = "tian_2021_crispra.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/TianKampmann2021_CRISPRa.h5ad?download=1",
+            url="https://zenodo.org/records/10044268/files/TianKampmann2021_CRISPRa.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1311,10 +1313,10 @@ def tian_2021_crispri() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "tian_2021_crispri.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/TianKampmann2021_CRISPRi.h5ad?download=1",
+            url="https://zenodo.org/records/10044268/files/TianKampmann2021_CRISPRi.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1338,10 +1340,10 @@ def weinreb_2020() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "weinreb_2020.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/WeinrebKlein2020.h5ad?download=1",
+            url="https://zenodo.org/records/10044268/files/WeinrebKlein2020.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1366,10 +1368,10 @@ def xie_2017() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "xie_2017.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/XieHon2017.h5ad?download=1",
+            url="https://zenodo.org/records/10044268/files/XieHon2017.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1396,10 +1398,10 @@ def zhao_2021() -> AnnData:  # pragma: no cover
         :class:`~anndata.AnnData` object of scPerturb prepared single-cell perturbation data
     """
     output_file_name = "zhaoSims2021.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
-            url="https://zenodo.org/record/7278143/files/ZhaoSims2021.h5ad?download=1",
+            url="https://zenodo.org/records/10044268/files/ZhaoSims2021.h5ad?download=1",
             output_file_name=output_file_name,
             output_path=settings.datasetdir,
             is_zip=False,
@@ -1410,15 +1412,18 @@ def zhao_2021() -> AnnData:  # pragma: no cover
 
 
 def cinemaot_example() -> AnnData:  # pragma: no cover:
-    """CINEMA-OT Example dataset.
+    """Subsampled CINEMA-OT example dataset.
+
+    Ex vivo stimulation of human peripheral blood mononuclear cells (PBMC) with interferon. This is a subsampled
+    dataset containing 1000 cells, either without stimulation or stimulated with IFNb. The full dataset is available
+    via the cinemaot_full() function.
 
-    Ex vivo stimulation of human peripheral blood mononuclear cells (PBMC) with interferon.
 
     Returns:
         :class:`~anndata.AnnData` object of PBMCs stimulated with interferon.
     """
     output_file_name = "cinemaot_example.h5ad"
-    output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
+    output_file_path = settings.datasetdir / output_file_name
     if not Path(output_file_path).exists():
         _download(
             url="https://figshare.com/ndownloader/files/42362796?private_link=270b0d2c7f1ea57c366d",
@@ -1429,3 +1434,167 @@ def cinemaot_example() -> AnnData:  # pragma: no cover:
     adata = sc.read_h5ad(output_file_path)
 
     return adata
+
+
+def dong_2023() -> AnnData:  # pragma: no cover
+    """Complete CINEMA-OT dataset.
+
+    Ex vivo stimulation of human peripheral blood mononuclear cells (PBMC) with interferon. This is the full dataset
+    containing 9209 cells that were stimulated with IFNb, IFNg, IFNb+IFNg, or left unstimulated. A subsampled version
+    of the dataset is available via cinemaot_example().
+
+    References:
+        Preprint: https://doi.org/10.1101/2022.07.31.502173
+        Dataset available here: https://datadryad.org/stash/dataset/doi:10.5061/dryad.4xgxd25g1
+
+    Returns:
+        :class:`~anndata.AnnData` object of PBMCs stimulated with interferon.
+    """
+    output_file_name = "dong_2023.h5ad"
+    output_file_path = settings.datasetdir / output_file_name
+    if not Path(output_file_path).exists():
+        _download(
+            url="https://figshare.com/ndownloader/files/43068190",
+            output_file_name=output_file_name,
+            output_path=settings.datasetdir,
+            is_zip=False,
+        )
+    adata = sc.read_h5ad(output_file_path)
+
+    return adata
+
+
+def smillie_2019() -> AnnData:  # pragma: no cover
+    """scRNA-seq data of the small intestine of mice under Ulcerative Colitis.
+
+    The resulting AnnData when preparing this dataset for processing with tascCODA is available via tasccoda_example().
+
+    References:
+        Smillie, Christopher S et al. “Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.”
+        Cell vol. 178,3 (2019): 714-730.e22. doi:10.1016/j.cell.2019.06.029
+
+    Returns:
+        :class:`~anndata.AnnData` object of the dataset.
+    """
+    output_file_name = "smillie_2019.h5ad.zip"
+    output_file_path = settings.datasetdir / Path(output_file_name).with_suffix("")
+    if not Path(output_file_path).exists():
+        _download(
+            url="https://figshare.com/ndownloader/files/43317285",
+            output_file_name=output_file_name,
+            output_path=settings.datasetdir,
+            is_zip=True,
+        )
+    adata = sc.read_h5ad(output_file_path)
+
+    return adata
+
+
+def combosciplex() -> AnnData:  # pragma: no cover
+    """scRNA-seq subset of the combinatorial experiment of sciplex3.
+
+    References:
+        Srivatsan SR et al., Trapnell C. Massively multiplex chemical transcriptomics at
+        single-cell resolution. Science. 2020 Jan 3;367(6473):45-51.
+        doi: 10.1126/science.aax6234. Epub 2019 Dec 5. PMID: 31806696; PMCID: PMC7289078.
+
+    Returns:
+        :class:`~anndata.AnnData` object of the dataset.
+    """
+    output_file_name = "combosciplex.h5ad"
+    output_file_path = settings.datasetdir / output_file_name
+    if not Path(output_file_path).exists():
+        _download(
+            url="https://figshare.com/ndownloader/files/44229635",
+            output_file_name=output_file_name,
+            output_path=settings.datasetdir,
+            is_zip=False,
+        )
+    adata = sc.read_h5ad(output_file_path)
+
+    return adata
+
+
+def sciplex_gxe1() -> AnnData:  # pragma: no cover
+    """sci-Plex-GxE combined chemical and genetic profiling of A172 dCas9-KRAB cells
+    genetically perturbed for HPRT1 or mismtach repair genes exposed to 6-thioguanine and temozolomide,
+    respectively, and A172 dCas9-SunTag cells genetically perturbed for HPRT1 exposed to 6-thioguanine.
+
+    References:
+        McFaline-Figueroa JL et al., Trapnell C. Multiplex single-cell chemical genomics reveals
+        the kinase dependence of the response to targeted therapy. Cell Genomics. 2024 Volume 4, Issue 2.
+        doi: 10.1016/j.xgen.2023.100487
+
+    Returns:
+        :class:`~anndata.AnnData` object of the dataset.
+    """
+    output_file_name = "sciPlexGxE_1_GSM7056148.h5ad"
+    output_file_path = settings.datasetdir / output_file_name
+    if not Path(output_file_path).exists():
+        _download(
+            url="https://figshare.com/ndownloader/files/45372454",
+            output_file_name=output_file_name,
+            output_path=settings.datasetdir,
+            is_zip=False,
+        )
+    adata = sc.read_h5ad(output_file_path)
+
+    return adata
+
+
+def zhang_2021() -> AnnData:  # pragma: no cover
+    """Single-cell RNA-seq of TNBC patients' immune cells exposed to paclitaxel alone or combined with the anti-PD-L1 atezolizumab.
+
+    This analysis, involving 22 patients, identifies immune subtypes predictive of therapeutic
+    responses and underscores potential limitations of combining paclitaxel with atezolizumab in treatment protocols.
+
+    The script that generated this specific AnnData object:
+    https://github.com/tessadgreen/ThesisCode/blob/main/Chapter3/drug_response/import_zhang_data.ipynb
+
+    This dataset does not contain the single-cell ATAC-seq data that was also measured for the paper.
+
+    References:
+        Zhang Y et al., Liu Z. Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer.
+        Cancer Cell. 2021 Volume 39, Issue 12. doi: https://doi.org/10.1016/j.ccell.2021.09.010
+
+    Returns:
+        :class:`~anndata.AnnData` object of the dataset.
+    """
+    output_file_name = "zhang_2021.h5ad"
+    output_file_path = settings.datasetdir / output_file_name
+    if not Path(output_file_path).exists():
+        _download(
+            url="https://figshare.com/ndownloader/files/46457872",
+            output_file_name=output_file_name,
+            output_path=settings.datasetdir,
+            is_zip=False,
+        )
+    adata = sc.read_h5ad(output_file_path)
+
+    return adata
+
+
+def hagai_2018() -> AnnData:  # pragma: no cover
+    """Cross-species analysis of primary dermal fibroblasts and bone marrow-derived phagocytes, stimulated with dsRNA and IFNB.
+
+    The study explores immune response variations across humans, macaques, mice, and rats.
+
+    Referenences:
+        Hagai, T., Chen, X., Miragaia, R.J. et al. Gene expression variability across cells and species shapes innate immunity.
+        Nature 563, 197–202 (2018). https://doi.org/10.1038/s41586-018-0657-2
+
+    Returns:
+        :class:`~anndata.AnnData` object of the dataset.
+    """
+    output_file_name = "hagai_2018.h5ad"
+    output_file_path = settings.datasetdir / output_file_name
+    if not Path(output_file_path).exists():
+        _download(
+            url="https://figshare.com/ndownloader/files/46978846",
+            output_file_name=output_file_name,
+            output_path=settings.datasetdir,
+            is_zip=False,
+        )
+    adata = sc.read_h5ad(output_file_path)
+
+    return adata