upload zebrafish perturb data

src/regvelo/datasets/_datasets.py

@@ -8,6 +8,7 @@
 # Remote data URLs
 url_adata = "https://drive.google.com/uc?id=1Nzq1F6dGw-nR9lhRLfZdHOG7dcYq7P0i&export=download"
 url_grn = "https://drive.google.com/uc?id=1ci_gCwdgGlZ0xSn6gSa_-LlIl9-aDa1c&export=download/"
+url_perturb = "https://drive.usercontent.google.com/download?id=1CKADDykadX0CLjYGPgc3YXA-AGRSaA1k&export=download&authuser=1&confirm=t&uuid=37eebdae-5f53-4e53-8d60-a5f52b528720&at=ALBwUgk1uT7pQx7RpXiGyK2yFpBI:1777810924901"
 
 url_adata_murine_processed = "https://drive.usercontent.google.com/download?id=19bNQfW3jMKEEjpjNdUkVd7KDTjJfqxa5&export=download&authuser=1&confirm=t&uuid=4fdf3051-229b-4ce2-b644-cb390424570a&at=APcmpoxgcuZ5r6m6Fb6N_2Og6tEO:1745354679573"
 url_adata_murine_normalized = "https://drive.usercontent.google.com/download?id=1xy2FNYi6Y2o_DzXjRmmCtARjoZ97Ro_w&export=download&authuser=1&confirm=t&uuid=12cf5d23-f549-48d9-b7ec-95411a58589f&at=APcmpoyexgouf243lNygF9yRUkmi:1745997349046"
@@ -63,6 +64,33 @@ def zebrafish_grn(file_path: str | Path = "data/zebrafish_nc/prior_GRN.csv") ->
     grn.to_csv(file_path)
     return grn
 
+def zebrafish_perturb(file_path: str | Path = "data/zebrafish_nc/perturbseq_all.h5ad") -> AnnData:                          
+      r"""Load zebrafish neural crest Perturb-seq dataset.                      
+
+      This dataset contains single-cell CRISPR screening (Perturb-seq) data from zebrafish neural crest (NC) cells, comprising 12,393 cells and 27,599 genes across 9 pooled samples. Cells were perturbed with sgRNAs targeting 22 transcription factors — including ETS-family members (*fli1a*, *elk3*, *erf*, *etv2*, *ets1*, *elf1*), pigment regulators (*mitfa*, *tfec*, *tfeb*), and additional NC regulators (*nr2f2*, *nr2f5*, *rarga*, *rxraa*, *smarcc1a*, *ebf3a*) — as well as combinatorial double or triple knockouts. Unperturbed control and negative-control cells are also included.
+
+      Cell type annotations span the major stages of NC development:
+
+      - Neural plate border (NPB) progenitors (``NPB_hox``, ``NPB_nohox``),     
+      - Migratory NC cells across axial levels (``mNC_arch1``, ``mNC_arch2``, ``mNC_head_mesenchymal``, ``mNC_hox34``, ``mNC_nohox``, ``mNC_trunk``, ``mNC_vagal``),                                                         
+      - Differentiating NC cells (``dNC_hox34``, ``dNC_nohox``),                
+      - Pigment cell lineages (``Pigment``, ``Pigment_1``, ``Pigment_gch2_high``), and                                                   
+      - Mutant populations (``Mutant``, ``Mutant_hox23``).
+
+      The object includes PCA, PHATE, and t-SNE embeddings, as well as imputed latent time and terminal state assignments.                               
+
+      Parameters  
+      ----------                                                                
+      file_path   
+          Path to local dataset. Will download from remote URL if not found.
+
+      Returns
+      -------                                                                   
+      Annotated data object of zebrafish NC Perturb-seq cells.
+      """                                                                       
+      adata = read(file_path, backup_url=url_perturb, sparse=True, cache=True)
+      return adata
+
 def murine_nc(data_type: Literal["preprocessed", "normalized", "velocyto"] = "preprocessed") -> AnnData:
     r"""Load mouse neural crest single-cell RNA-seq dataset (subset of Qiu et al.).