diff --git a/sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/__init__.py b/sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/__init__.py new file mode 100644 index 000000000..b1d5b2c2b --- /dev/null +++ b/sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/__init__.py @@ -0,0 +1 @@ +FILE_PATH = __file__ diff --git a/sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/musmusculus_x_2022_x_yim_001.py b/sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/musmusculus_x_2022_x_yim_001.py new file mode 100644 index 000000000..8fec7a6bb --- /dev/null +++ b/sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/musmusculus_x_2022_x_yim_001.py @@ -0,0 +1,15 @@ +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 diff --git a/sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/musmusculus_x_2022_x_yim_001.yaml b/sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/musmusculus_x_2022_x_yim_001.yaml new file mode 100644 index 000000000..d37e7e7a9 --- /dev/null +++ b/sfaira/data/dataloaders/loaders/d10_1038_s41593_021_01005_1/musmusculus_x_2022_x_yim_001.yaml @@ -0,0 +1,97 @@ +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"