Skip to content

Updated cxg_annotate_graph_v2.py #11

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
Caroline-99 wants to merge 9 commits into from
Closed

Updated cxg_annotate_graph_v2.py #11

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
afe98ee
modified the graph_v2 script to process the folder and tested it with…
Caroline-99 Nov 5, 2025
ff50014
Add gpt-4.1 as model
ubyndr Nov 7, 2025
c63d025
Update caching for multiple input datasets
ubyndr Nov 7, 2025
eda4759
Update expansion caching logic
ubyndr Nov 10, 2025
dccaf9e
Tested 30 datasets, agent created a script to assess the granularity …
Caroline-99 Nov 12, 2025
d993b02
added a notebook analysis example of 30 CxG datasets
Caroline-99 Nov 14, 2025
0a361cd
Update amica_granularity_showcase.ipynb
Caroline-99 Nov 14, 2025
3c121f3
updated the notebook to include "broad term" filtering results
Caroline-99 Dec 11, 2025
0482256
added tissue context results
Caroline-99 Dec 11, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
The table of contents is too big for display.
Diff view
Diff view
  •  
  •  
  •  
1 change: 1 addition & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ htmlcov/
.coverage
.coverage.*
.cache
cache/
nosetests.xml
coverage.xml
*.cover
Expand Down
2,129 changes: 2,129 additions & 0 deletions Notebooks/amica_granularity_showcase.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

2 changes: 2 additions & 0 deletions cellsem_agent/agents/annotator/annotator_agent.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
"""
Ontology based Annotator Agent.
"""

import logging
from typing import List, Optional

Expand Down Expand Up @@ -135,6 +136,7 @@ class TextAnnotationResult(BaseModel):

annotator_agent = Agent(
model="openai:gpt-5",
# model="openai:gpt-4.1",
# model="openai:gpt-4o",
# model="openai:gpt-4o-2024-11-20",
deps_type=AnnotatorDependencies,
Expand Down
29 changes: 22 additions & 7 deletions cellsem_agent/agents/paper_celltype/paper_celltype_agent.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,20 +1,21 @@
"""
Agent for Cell Ontology.
"""

import logging
from pydantic_ai import Agent

cell_logger = logging.getLogger(__name__)
cell_logger.setLevel(logging.INFO)
console = logging.StreamHandler()
console.setLevel(logging.INFO)
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
console.setFormatter(formatter)
cell_logger.addHandler(console)

cell_logger.propagate = False

from .paper_celltype_config import PaperCTDependencies
from .paper_celltype_config import PaperCTDependencies
from .paper_celltype_tools import get_full_text, read_json

SYSTEM_PROMPT = """
Expand All @@ -35,17 +36,31 @@
from pydantic import BaseModel, Field
from typing import List, Optional


class CellTypeEntry(BaseModel):
name: str = Field(..., description="The exact cc.label from the input JSON.")
full_name: Optional[str] = Field(None, description="The expanded or reconstructed full name of the cell type as defined in the paper.")
paper_synonyms: Optional[str] = Field(None, description="Synonyms mentioned in the paper, separated by semicolons.")
tissue_context: Optional[str] = Field(None, description="Exact quoted tissue(s) or anatomical terms from the paper where the cell type was identified.")
full_name: Optional[str] = Field(
None,
description="The expanded or reconstructed full name of the cell type as defined in the paper.",
)
paper_synonyms: Optional[str] = Field(
None, description="Synonyms mentioned in the paper, separated by semicolons."
)
tissue_context: Optional[str] = Field(
None,
description="Exact quoted tissue(s) or anatomical terms from the paper where the cell type was identified.",
)


class BiocurationOutput(BaseModel):
cell_type_annotations: List[CellTypeEntry] = Field(..., description="A list of extracted cell type annotations.")
cell_type_annotations: List[CellTypeEntry] = Field(
..., description="A list of extracted cell type annotations."
)


celltype_agent = Agent(
model="openai:gpt-5",
# model="openai:gpt-4.1",
# model="openai:gpt-4o-2024-11-20",
deps_type=PaperCTDependencies,
result_type=BiocurationOutput,
Expand All @@ -54,4 +69,4 @@ class BiocurationOutput(BaseModel):
)

# celltype_agent.tool(get_full_text)
# celltype_agent.tool(read_json)
# celltype_agent.tool(read_json)
46 changes: 46 additions & 0 deletions .../cxg_annotate/amica_test_data/019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
author_cell_type CL_label CL_ID reference dataset_version
SI_earlyAE enterocyte of epithelium of small intestine CL:1000334 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_AE2 enterocyte of epithelium of small intestine CL:1000334 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_tuft intestinal tuft cell CL:0019032 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
C_earlyACC enterocyte of epithelium of large intestine CL:0002071 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
C_goblet colon goblet cell CL:0009039 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_matureAE enterocyte of epithelium of small intestine CL:1000334 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
C_BEST4 BEST4+ enterocyte CL:4030026 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_intermAE enterocyte of epithelium of small intestine CL:1000334 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
C_lateACC enterocyte of epithelium of large intestine CL:0002071 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_goblet small intestine goblet cell CL:1000495 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
C_EEC enteroendocrine cell of colon CL:0009042 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
C_tuft tuft cell of colon CL:0009041 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
C_ISC intestinal crypt stem cell of colon CL:0009043 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_ISC intestinal crypt stem cell of small intestine CL:0009017 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_BEST4 epithelial cell of small intestine CL:0002254 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_TA transit amplifying cell of small intestine CL:0009012 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
C_TA transit amplifying cell of colon CL:0009011 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_secretory_prog progenitor cell CL:0011026 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
C_secretory_prog progenitor cell CL:0011026 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_EEC enteroendocrine cell of small intestine CL:0009006 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_TA2 transit amplifying cell of small intestine CL:0009012 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_paneth paneth cell of epithelium of small intestine CL:1000343 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_FAE microfold cell of epithelium of small intestine CL:1000353 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
absorptive enterocyte of epithelium of small intestine CL:1000334 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
tuft intestinal tuft cell CL:0019032 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
absorptive enterocyte of epithelium of large intestine CL:0002071 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
goblet colon goblet cell CL:0009039 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
BEST4+ BEST4+ enterocyte CL:4030026 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
goblet small intestine goblet cell CL:1000495 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
EEC enteroendocrine cell of colon CL:0009042 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
tuft tuft cell of colon CL:0009041 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
ISC intestinal crypt stem cell of colon CL:0009043 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
ISC intestinal crypt stem cell of small intestine CL:0009017 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
BEST4+ epithelial cell of small intestine CL:0002254 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
TA transit amplifying cell of small intestine CL:0009012 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
TA transit amplifying cell of colon CL:0009011 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
secretory_prog progenitor cell CL:0011026 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
EEC enteroendocrine cell of small intestine CL:0009006 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
paneth paneth cell of epithelium of small intestine CL:1000343 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
FAE microfold cell of epithelium of small intestine CL:1000353 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_6-? enterocyte of epithelium of small intestine CL:1000334 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
C_earlyCC enterocyte of epithelium of large intestine CL:0002071 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
C_lateCC enterocyte of epithelium of large intestine CL:0002071 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_secretory small intestine goblet cell CL:1000495 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
SI_secretory paneth cell of epithelium of small intestine CL:1000343 https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad
46 changes: 46 additions & 0 deletions .../cxg_annotate/amica_test_data/02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
author_cell_type CL_label CL_ID reference dataset_version
cvLSEC endothelial cell of pericentral hepatic sinusoid CL:0019022 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
LAM-like macrophage CL:0000235 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
lrNK hepatic pit cell CL:2000054 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
C-Hepato2 centrilobular region hepatocyte CL:0019029 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Arterial endothelial cell of artery CL:1000413 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
I-Hepato midzonal region hepatocyte CL:0019028 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
CD8T CD8-positive, alpha-beta T cell CL:0000625 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
P-Hepato periportal region hepatocyte CL:0019026 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
ppLSEC endothelial cell of periportal hepatic sinusoid CL:0019021 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Kupffer Kupffer cell CL:0000091 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
ActMac macrophage CL:0000235 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
CD4T CD4-positive, alpha-beta T cell CL:0000624 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
CD3T-lrNK hepatic pit cell CL:2000054 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
C-Hepato centrilobular region hepatocyte CL:0019029 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
MHCII macrophage CL:0000235 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
CD8T-cNK natural killer cell CL:0000623 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Stellate hepatic stellate cell CL:0000632 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Kupffer--LSEC-Doublet unknown unknown https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Tcell T cell CL:0000084 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Neutrophil neutrophil CL:0000775 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Chol intrahepatic cholangiocyte CL:0002538 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
cNK natural killer cell CL:0000623 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
cDC conventional dendritic cell CL:0000990 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Hepato hepatocyte CL:0000182 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
P-Hepato2 periportal region hepatocyte CL:0019026 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
cvLSEC--T-Doublet unknown unknown https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
cvEndo vein endothelial cell CL:0002543 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Monocyte monocyte CL:0000576 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Prolif unknown unknown https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
AntiB plasma cell CL:0000786 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
NKT--Mac-Doublet unknown unknown https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
CholMucus intrahepatic cholangiocyte CL:0002538 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
MatB mature B cell CL:0000785 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Fibroblast fibroblast CL:0000057 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Hepato--Mac unknown unknown https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
pDC plasmacytoid dendritic cell CL:0000784 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Mac--Fibro-Doublet unknown unknown https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
RBC erythrocyte CL:0000232 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
MAST mast cell CL:0000097 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
MatB--CD4T-Doublet unknown unknown https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Mac--B-Doublet unknown unknown https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
MatB--RBC unknown unknown https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
CD4T--RBC-Doublet unknown unknown https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
cNK--RBC-Doublet unknown unknown https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
NKT natural killer cell CL:0000623 https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad
Loading
Loading