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Kassandra-cell-deconvolution
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---
license: other
datasets:
- bostongene/Kassandra-data
---

---
![](https://huggingface.co/bostongene/Kassandra-cell-deconvolution/resolve/main/kassandra_logo.png)
# Kassandra: Cell Deconvolution Tool from RNA-seq

*Precise reconstruction of the tumor microenvironment using bulk RNA-seq and a unique machine learning-based algorithm trained on artificial transcriptomes* 

* [HuggingFace Spaces Tool](https://bostongene-kassandra.hf.space/)
* [HuggingFace Dataset](https://huggingface.co/datasets/bostongene/Kassandra-data)
* [Article](https://www.cell.com/cancer-cell/fulltext/S1535-6108(22)00319-1)
* [GitHub](https://github.com/BostonGene/Kassandra)

Here, we present Kassandra, a robust and accurate cell deconvolution tool developed for analysis of healthy tissue and tumor biopsies. Based on RNA-seq NGS data of a biological sample, Kassandra predicts cellular composition including stromal and immune elements by analyzing the gene expression. This will lead to an improved understanding of the tumor microenvironment, which is a critical factor in cancer pathogenesis, clinical outcome, and therapeutic resistance.

Kassandra is a decision tree machine learning-algorithm trained on a collection of over thousands of RNA profiles from various sorted cell types. Performance was validated on over 4,000 H&E tissue slides and more than 1,000 samples comprising normal and tumor tissues by comparison with cytometric, immunohistochemical or single-cell RNA sequencing measurements of the same tissue.

![](https://huggingface.co/bostongene/Kassandra-cell-deconvolution/resolve/main/visual_abstract.png)


### Data used in model training
- [Collection of 9056 bulk RNA-seq samples from 505 datasets of sorted cells, cancer cells and cell lines](https://huggingface.co/datasets/bostongene/Kassandra-data/resolve/main/train_data/all_models.zip)
- [348 bulk RNA-seq samples of sorted cell populations (including 343 samples of cells from the blood)](https://huggingface.co/datasets/bostongene/Kassandra-data/resolve/main/train_data/laboratory_data.zip)
### Validation data and cell predictions
- [45 bulk RNA-seq of PBMC or PB samples paired with cytometry data](https://huggingface.co/datasets/bostongene/Kassandra-data/resolve/main/validation_data/BG_blood.zip)
- [Collection of 1750 blood bulk RNA-seq samples from 42 datasets from healthy donors](https://huggingface.co/datasets/bostongene/Kassandra-data/resolve/main/validation_data/SRA_healthy_donors.zip)
- [24 validation datasets with 1092 RNA-seq samples paired with flow cytometry, hematological analyzer, CyTOF or other cell percentage data](https://huggingface.co/datasets/bostongene/Kassandra-data/resolve/main/validation_data/validation_datasets.zip)
- [Tumor tissues from TCGA project predicted by Kassandra and other algorithms (CIBERSORT, CIBERSORTX, quantiseq, fardeep, ABIS, EPIC, MCP-counter, xcell, Scaden (PBMC))](https://huggingface.co/datasets/bostongene/Kassandra-data/resolve/main/validation_data/TCGA.zip)
- [Tissues from GTEX project predicted by Kassandra](https://huggingface.co/datasets/bostongene/Kassandra-data/resolve/main/validation_data/GTEX.zip)
## Licencse
BY UTILIZING THE CODE, YOU ARE CONSENTING TO BE AND AGREE TO BE BOUND BY ALL OF THE TERMS OF THIS LIMITED LICENSE, SEE "LICENSE"