|
|
|
import streamlit as st |
|
|
|
from constants import MODELS |
|
|
|
st.set_page_config(layout="wide") |
|
|
|
st.markdown( |
|
""" |
|
# Download & Credits |
|
|
|
## 1. Preprocessing pipelines |
|
|
|
- Downloading datasets: [nf-core/fetchngs (revision 1.10.0)](https://github.com/nf-core/fetchngs) |
|
- Aligning datasets: [brickmanlab/scrnaseq (revision: feature/smartseq)](https://github.com/brickmanlab/scrnaseq) |
|
- **Ensembl Genomes (models <= v1.1)** |
|
- Mouse: GRCm38 v102 |
|
- Human: GRCh38 v110 |
|
|
|
## 2. Codebase |
|
|
|
- Data analysis: [brickmanlab/proks-salehin-et-al](https://github.com/brickmanlab/proks-salehin-et-al) |
|
- Web portal on HF: [brickmanlab/hf-preimplantation-portal](https://huggingface.co/spaces/brickmanlab/hf-preimplantation-portal/tree/main) |
|
- Web portal (deprecated): [brickmanlab/preimplantation-portal](https://github.com/brickmanlab/preimplantation-portal) |
|
|
|
## 3. Raw and normalized counts |
|
|
|
Raw counts are stored in `layers['counts']` and normalized counts are stored in `.X`. |
|
|
|
- **models <= v1.1** |
|
- [mouse](https://zenodo.org/records/13749348/files/01_mouse_reprocessed.h5ad) |
|
- [human](https://zenodo.org/records/13749348/files/32_human_adata.h5ad) |
|
|
|
## 4. scVI/scANVI models |
|
|
|
Trained models with parameters were uploaded to [Hugging Face](https://huggingface.co/brickmanlab/preimplantation-models). |
|
""" |
|
) |
|
|
|
text = "" |
|
for specie in MODELS: |
|
text += f"- **{specie}**: " |
|
for version in MODELS[specie]: |
|
url = ( |
|
f"https://huggingface.co/brickmanlab/{specie.lower()}-scanvi/tree/{version}" |
|
) |
|
text += f"[{version}]({url}), " |
|
text = text[:-2] + "\n" |
|
st.markdown(text) |
|
|
|
st.markdown( |
|
""" |
|
## 5. Credit |
|
|
|
> [!TIP] |
|
> Proks, M., Salehin, N. & Brickman, J.M. Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing. Nat Methods 22, 207–216 (2025). https://doi.org/10.1038/s41592-024-02511-3 |
|
""" |
|
) |
|
|
