10_1038_s41593_021_01005_1

sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/__init__.py

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+FILE_PATH = __file__

sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/musmusculus_x_2022_x_yim_001.py

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+import anndata
+import os
+import scipy.sparse
+
+def load(data_dir,sample_fn, **kwargs):
+    import anndata2ri
+    from rpy2.robjects import r
+    anndata2ri.activate()
+    fn = os.path.join(data_dir, sample_fn)
+    adata = r(
+        f"library(Seurat)\n"
+        f"new_obj = readRDS('{fn}')))\n"
+        f"as.SingleCellExperiment(new_obj)\n"
+    )
+    return adata

sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/musmusculus_x_2022_x_yim_001.yaml

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+dataset_structure:
+    dataset_index: 1
+    sample_fns:
+        - "GSE182098_immune-cell_single-cell-atlas-15Jan2021.RDS"
+        - "GSE182098_peripheral-nerves_single-nuclei-atlas-22Jan2021.RDS"
+        - "GSE182098_peripheral-nerves-Schwann-cell-specific_single-nuclei-atlas-8Feb2021.RDS"
+        - "GSE182098_schwann_cell_single-nuclei-atlas-12Jan2021.RDS"
+        - "GSE182098_sciatic-nerve_single-nuclei-atlas-16Dec2020.RDS"
+dataset_wise:
+    author: "Yim, Aldrin K.Y."
+    default_embedding:
+    doi_preprint:
+    doi_journal: "10.1038/s41593-021-01005-1"
+    download_url_data:
+      - "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE182098&format=file&file=GSE182098%5Fimmune%2Dcell%5Fsingle%2Dcell%2Datlas%2D15Jan2021%2ERDS%2Egz"
+      - "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE182098&format=file&file=GSE182098%5Fperipheral%2Dnerves%2DSchwann%2Dcell%2Dspecific%5Fsingle%2Dnuclei%2Datlas%2D8Feb2021%2ERDS%2Egz"
+      - "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE182098&format=file&file=GSE182098%5Fperipheral%2Dnerves%5Fsingle%2Dnuclei%2Datlas%2D22Jan2021%2ERDS%2Egz"
+      - "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE182098&format=file&file=GSE182098%5Fschwann%5Fcell%5Fsingle%2Dnuclei%2Datlas%2D12Jan2021%2ERDS%2Egz"
+      - "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE182098&format=file&file=GSE182098%5Fsciatic%2Dnerve%5Fsingle%2Dnuclei%2Datlas%2D16Dec2020%2ERDS%2Egz"
+    download_url_meta:
+    primary_data: True
+    year: 2022
+layers:
+    layer_counts: "RNA"
+    layer_processed: "SCT"
+    layer_spliced_counts:
+    layer_spliced_processed:
+    layer_unspliced_counts:
+    layer_unspliced_processed:
+    layer_velocity:
+dataset_or_feature_wise:
+    feature_reference: "mm10"
+    feature_reference_var_key:
+    feature_type: "rna"
+    feature_type_var_key:
+dataset_or_observation_wise:
+    assay_sc:
+    assay_sc_obs_key: "rep"
+    assay_differentiation:
+    assay_differentiation_obs_key:
+    assay_type_differentiation:
+    assay_type_differentiation_obs_key:
+    bio_sample:
+    bio_sample_obs_key:
+    cell_line:
+    cell_line_obs_key:
+    cell_type:
+    cell_type_obs_key:
+    development_stage: "early adult stage"
+    development_stage_obs_key:
+    disease: "none"
+    disease_obs_key:
+    ethnicity:
+    ethnicity_obs_key:
+    gm:
+    gm_obs_key:
+    individual:
+    individual_obs_key:
+    organ:
+    organ_obs_key:
+    organism: "Mus musculus"
+    organism_obs_key:
+    sample_source: "primary_tissue"
+    sample_source_obs_key:
+    sex:
+    sex_obs_key:
+    source_doi:
+    source_doi_obs_key:
+    state_exact:
+    state_exact_obs_key:
+    tech_sample:
+    tech_sample_obs_key:
+    treatment:
+    treatment_obs_key:
+feature_wise:
+    feature_id_var_key:
+    feature_symbol_var_key: "index"
+observation_wise:
+    spatial_x_coord_obs_key:
+    spatial_y_coord_obs_key:
+    spatial_z_coord_obs_key:
+    vdj_vj_1_obs_key_prefix:
+    vdj_vj_2_obs_key_prefix:
+    vdj_vdj_1_obs_key_prefix:
+    vdj_vdj_2_obs_key_prefix:
+    vdj_c_call_obs_key_suffix:
+    vdj_consensus_count_obs_key_suffix:
+    vdj_d_call_obs_key_suffix:
+    vdj_duplicate_count_obs_key_suffix:
+    vdj_j_call_obs_key_suffix:
+    vdj_junction_obs_key_suffix:
+    vdj_junction_aa_obs_key_suffix:
+    vdj_locus_obs_key_suffix:
+    vdj_productive_obs_key_suffix:
+    vdj_v_call_obs_key_suffix:
+meta:
+    version: "1.2"