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10_1038_s41591_019_0750_6 #599

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6c524a9
try dataloader
dlhlisa Feb 15, 2022
cdb9536
remove raw data
dlhlisa Feb 16, 2022
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1 change: 1 addition & 0 deletions sfaira/data/dataloaders/loaders/d10_1038_s41591_019_0750_6/__init__.py
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FILE_PATH = __file__
11 changes: 11 additions & 0 deletions sfaira/data/dataloaders/loaders/d10_1038_s41591_019_0750_6/lung_x_2020_x_laughney_001.py
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import anndata
import os
import scipy.sparse


def load(data_dir, sample_fn, **kwargs):
fn = os.path.join(data_dir, sample_fn)
adata = anndata.read(fn)
adata.X = scipy.sparse.csr_matrix(adata.X)

return adata
178 changes: 178 additions & 0 deletions sfaira/data/dataloaders/loaders/d10_1038_s41591_019_0750_6/lung_x_2020_x_laughney_001.yaml
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dataset_structure:
dataset_index: 1
sample_fns:
- "GSM3516662_MSK_LX653_PRIMARY_TUMOUR_dense.csv.gz"
- "GSM3516663_MSK_LX661_PRIMARY_TUMOUR_dense.csv.gz"
- "GSM3516664_MSK_LX666_METASTASIS_dense.csv.gz"
- "GSM3516665_MSK_LX675_PRIMARY_TUMOUR_dense.csv.gz"
- "GSM3516666_MSK_LX675_NORMAL_dense.csv.gz"
- "GSM3516667_MSK_LX676_PRIMARY_TUMOUR_dense.csv.gz"
- "GSM3516668_MSK_LX255B_METASTASIS_dense.csv.gz"
- "GSM3516669_MSK_LX679_PRIMARY_TUMOUR_dense.csv.gz"
- "GSM3516670_MSK_LX680_PRIMARY_TUMOUR_dense.csv.gz"
- "GSM3516671_MSK_LX681_METASTASIS_dense.csv.gz"
- "GSM3516672_MSK_LX682_PRIMARY_TUMOUR_dense.csv.gz"
- "GSM3516673_MSK_LX682_NORMAL_dense.csv.gz"
- "GSM3516674_MSK_LX684_PRIMARY_TUMOUR_dense.csv.gz"
- "GSM3516675_MSK_LX684_NORMAL_dense.csv.gz"
- "GSM3516676_MSK_LX685_NORMAL_dense.csv.gz"
- "GSM3516677_MSK_LX699_METASTASIS_dense.csv.gz"
- "GSM3516678_MSK_LX701_METASTASIS_dense.csv.gz"
- "GSM3516679_MOUSE4585_kidneyDTC_dense.csv.gz"
- "GSM3516680_MOUSE4587_kidneyDTC_dense.csv.gz"
- "GSM3516681_MOUSE4774_01_lungIncipientMet_dense.csv.gz"
- "GSM3516682_MOUSE4774_02_lungIncipientMet_dense.csv.gz"
- "GSM3516683_MOUSE4766_lungMacromet_dense.csv.gz"
- "GSM3516684_MOUSE4768_lungMacromet_dense.csv.gz"
- "GSM3516685_MOUSE4770_lungMacromet_dense.csv.gz"
- "GSM3516686_MOUSE4531_antiGM1_boneMacromet_dense.csv.gz"
- "GSM3516687_MOUSE4531_antiGM1_kidneyMacromet_dense.csv.gz"
- "GSM3516688_MOUSE4544_antiGM1_kidneyMacromet_dense.csv.gz"
- "GSM3516689_MOUSE4548_antiGM1_boneMacromet_dense.csv.gz"
- "GSM3516690_MOUSE4737_antiGM1_boneMacromet_dense.csv.gz"
- "GSM3516691_MOUSE4737_antiGM1_kidneyMacromet_dense.csv.gz"
dataset_wise:
author: "Laughney, Ashley M."
default_embedding:
doi_preprint: "10.1038/s41591-019-0750-6"
doi_journal: "10.1038/s41591-019-0750-6"
download_url_data: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123904/suppl/GSE123904_RAW.tar"
download_url_meta:
primary_data: True
year: 2020
layers:
layer_counts: "counts"
layer_processed:
layer_spliced_counts:
layer_spliced_processed:
layer_unspliced_counts:
layer_unspliced_processed:
layer_velocity:
dataset_or_feature_wise:
feature_reference:
feature_reference_var_key:
feature_type: "rna"
feature_type_var_key:
dataset_or_observation_wise:
assay_sc:
"GSM3516662_MSK_LX653_PRIMARY_TUMOUR_dense.csv.gz": EFO:0010942
"GSM3516663_MSK_LX661_PRIMARY_TUMOUR_dense.csv.gz": EFO:0010942
"GSM3516664_MSK_LX666_METASTASIS_dense.csv.gz": EFO:0009708
"GSM3516665_MSK_LX675_PRIMARY_TUMOUR_dense.csv.gz": EFO:0010942
"GSM3516666_MSK_LX675_NORMAL_dense.csv.gz": EFO:0001986
"GSM3516667_MSK_LX676_PRIMARY_TUMOUR_dense.csv.gz": EFO:0010942
"GSM3516668_MSK_LX255B_METASTASIS_dense.csv.gz": EFO:0009708
"GSM3516669_MSK_LX679_PRIMARY_TUMOUR_dense.csv.gz": EFO:0010942
"GSM3516670_MSK_LX680_PRIMARY_TUMOUR_dense.csv.gz": EFO:0010942
"GSM3516671_MSK_LX681_METASTASIS_dense.csv.gz": EFO:0009708
"GSM3516672_MSK_LX682_PRIMARY_TUMOUR_dense.csv.gz": EFO:0010942
"GSM3516673_MSK_LX682_NORMAL_dense.csv.gz": EFO:0001986
"GSM3516674_MSK_LX684_PRIMARY_TUMOUR_dense.csv.gz": EFO:0010942
"GSM3516675_MSK_LX684_NORMAL_dense.csv.gz": EFO:0001986
"GSM3516676_MSK_LX685_NORMAL_dense.csv.gz": EFO:0001986
"GSM3516677_MSK_LX699_METASTASIS_dense.csv.gz": EFO:0009708
"GSM3516678_MSK_LX701_METASTASIS_dense.csv.gz": EFO:0009708
"GSM3516679_MOUSE4585_kidneyDTC_dense.csv.gz": UBERON:0002113
"GSM3516680_MOUSE4587_kidneyDTC_dense.csv.gz": UBERON:0002113
"GSM3516681_MOUSE4774_01_lungIncipientMet_dense.csv.gz": EFO:0009708
"GSM3516682_MOUSE4774_02_lungIncipientMet_dense.csv.gz": EFO:0009708
"GSM3516683_MOUSE4766_lungMacromet_dense.csv.gz": UBERON:0002048
"GSM3516684_MOUSE4768_lungMacromet_dense.csv.gz": UBERON:0002048
"GSM3516685_MOUSE4770_lungMacromet_dense.csv.gz": UBERON:0002048
"GSM3516686_MOUSE4531_antiGM1_boneMacromet_dense.csv.gz": UBERON:0001474
"GSM3516687_MOUSE4531_antiGM1_kidneyMacromet_dense.csv.gz": UBERON:0002113
"GSM3516688_MOUSE4544_antiGM1_kidneyMacromet_dense.csv.gz": UBERON:0002113
"GSM3516689_MOUSE4548_antiGM1_boneMacromet_dense.csv.gz": UBERON:0001474
"GSM3516690_MOUSE4737_antiGM1_boneMacromet_dense.csv.gz": UBERON:0001474
"GSM3516691_MOUSE4737_antiGM1_kidneyMacromet_dense.csv.gz": UBERON:0002113
assay_sc_obs_key:
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:
development_stage_obs_key:
disease:
# MONDO: 0008903
disease_obs_key:
ethnicity:
ethnicity_obs_key:
gm:
gm_obs_key:
individual:
individual_obs_key:
organ:
"GSM3516662_MSK_LX653_PRIMARY_TUMOUR_dense.csv.gz": "lung"
"GSM3516663_MSK_LX661_PRIMARY_TUMOUR_dense.csv.gz": "lung"
"GSM3516664_MSK_LX666_METASTASIS_dense.csv.gz": "lung"
"GSM3516665_MSK_LX675_PRIMARY_TUMOUR_dense.csv.gz": "lung"
"GSM3516666_MSK_LX675_NORMAL_dense.csv.gz": "lung"
"GSM3516667_MSK_LX676_PRIMARY_TUMOUR_dense.csv.gz": "lung"
"GSM3516668_MSK_LX255B_METASTASIS_dense.csv.gz": "lung"
"GSM3516669_MSK_LX679_PRIMARY_TUMOUR_dense.csv.gz": "lung"
"GSM3516670_MSK_LX680_PRIMARY_TUMOUR_dense.csv.gz": "lung"
"GSM3516671_MSK_LX681_METASTASIS_dense.csv.gz": "lung"
"GSM3516672_MSK_LX682_PRIMARY_TUMOUR_dense.csv.gz": "lung"
"GSM3516673_MSK_LX682_NORMAL_dense.csv.gz": "lung"
"GSM3516674_MSK_LX684_PRIMARY_TUMOUR_dense.csv.gz": "lung"
"GSM3516675_MSK_LX684_NORMAL_dense.csv.gz": "lung"
"GSM3516676_MSK_LX685_NORMAL_dense.csv.gz": "lung"
"GSM3516677_MSK_LX699_METASTASIS_dense.csv.gz": "lung"
"GSM3516678_MSK_LX701_METASTASIS_dense.csv.gz": "lung"
"GSM3516679_MOUSE4585_kidneyDTC_dense.csv.gz": "lung"
"GSM3516680_MOUSE4587_kidneyDTC_dense.csv.gz": "lung"
"GSM3516681_MOUSE4774_01_lungIncipientMet_dense.csv.gz": "lung"
"GSM3516682_MOUSE4774_02_lungIncipientMet_dense.csv.gz": "lung"
"GSM3516683_MOUSE4766_lungMacromet_dense.csv.gz": "lung"
"GSM3516684_MOUSE4768_lungMacromet_dense.csv.gz": "lung"
"GSM3516685_MOUSE4770_lungMacromet_dense.csv.gz": "lung"
"GSM3516686_MOUSE4531_antiGM1_boneMacromet_dense.csv.gz": "lung"
"GSM3516687_MOUSE4531_antiGM1_kidneyMacromet_dense.csv.gz": "lung"
"GSM3516688_MOUSE4544_antiGM1_kidneyMacromet_dense.csv.gz": "lung"
"GSM3516689_MOUSE4548_antiGM1_boneMacromet_dense.csv.gz": "lung"
"GSM3516690_MOUSE4737_antiGM1_boneMacromet_dense.csv.gz": "lung"
"GSM3516691_MOUSE4737_antiGM1_kidneyMacromet_dense.csv.gz": "lung"
organ_obs_key:
organism: "Homo sapiens"
organism_obs_key:
sample_source: "tumor"
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"