HIDE-deconv

Interactive command line tool and python package for hierarchical deconvolution and analysis of bulk RNA-seq data.

Features

• Designed for AnnData single cell datasets
• Open Source package, that can be run on safe servers
• Hierarchical cell type deconvolution for any number of cell type annotation layers
• Includes methods for post-deconvolution analysis
• Usable via command line interface and Python API
• Provides a guided workflow that allows users without programming experience to perform deconvolution

For a detailed overview of all features and usage, please read the Userguide

Installation

# Create and activate a new virtual environment (recommended)
python3 -m venv .venv
source .venv/bin/activate

# Install HIDE-deconv
pip install hide-deconv

Necessary Data

• Single-cell data: Annotated AnnData (.h5ad) file with gene names in adata.var_names and cell type annotations for each desired layer in adata.obs (at least one layer of cell type annotations is necessary).
• Bulk RNA-seq data: CSV file, genes as row index, samples as columns. Gene IDs must match single-cell data.
• Sample sheet (optional): CSV with sample meta-information (e.g., cohort, survival time, event).
• Data Normalization: We recommend to use raw counts for all datasets.

Command Line Workflow

Deconvolution (standard workflow):

hide-deconv run --path <project_dir>

This initializes the project, preprocesses data, trains the model, and runs deconvolution.

Difference in composition & survival analysis:

hide-deconv analyze diff --path <project_dir>
hide-deconv analyze survival --path <project_dir>

• For difference analysis, the sample sheet must contain columns for sample ID and cohort.
• For survival analysis, the sample sheet must contain columns for sample ID, survival time and event. Values in the event column must be either "1": event occured or "0": no event.

Command overview:

hide-deconv help

This displays a short introduction to the command line interface and gives an overview of all available commands.

Tutorials

Quick Deconvolution API Example

HIDE-deconv contains a "lazy" API for users who want quick access to deconvolution.

import anndata as ad
import pandas as pd
from hide_deconv import deconvolution

adata = ad.read_h5ad("single_cells.h5ad")
bulk = pd.read_csv("bulk.csv", index_col=0) # genes x samples

results = deconvolution(adata, bulk, celltype_cols=["cell_type", "major"]) # Two layer hierarchy
# results = deconvolution(adata, bulk, celltype_cols="major") # Deconvolution only on major level

# results is a list of pandas DataFrames, one per hierarchy layer
# results[0] is the finest layer, results[1] the next coarser layer

If you only pass adata and bulk, celltype_cols defaults to "cell_type".

Extended API Example

For experienced users offers HIDE-deconv a highly customizable API, where they can integrate their own preprocessing steps into the pipeline. An example is given below.

import anndata as ad
import pandas as pd
import numpy as np
from hide_deconv.preprocessing import (
	train_test_split_adata,
	create_reference,
	create_hierarchy,
	create_bulks,
)
from hide_deconv.models import HIDE
from hide_deconv.statistic import run_mann_whitney_u

# 1. Load AnnData
adata = ad.read_h5ad("single_cells.h5ad")

# 2. Split into training and test set
adata_train, adata_test = train_test_split_adata(adata, celltype_col="cell_type", train_frac=0.7)

# 3. Create reference profiles and hierarchy (single layer example)
X_sub = create_reference(adata_train, celltype_col="cell_type")
A_l = [pd.DataFrame(np.eye(X_sub.shape[1]), index=X_sub.columns, columns=X_sub.columns)]
X_l = [X_sub]

# 4. Simulate training bulks
Y_train, C_train = create_bulks(adata_train, n_bulks=1000, n_cells_per_bulk=100, celltype_col="cell_type")

# 5. Simulate test bulks
Y_test, C_test = create_bulks(adata_test, n_bulks=100, n_cells_per_bulk=100, celltype_col="cell_type")

# 6. Initialize and train model
hide = HIDE(X_l, A_l)
hide.train(Y_train, C_train, iter=1000)

# 7. Deconvolution on test data
results = hide.predict(Y_test, norm=True)["prediction"]

# 8. Optional: Difference in composition analysis
# (requires a sample sheet with columns 'SampleID' and 'Cohort')

# sample_sheet = read_csv("sample_sheet.csv")
# diff = run_mann_whitney_u(results[0], sample_sheet, sample_id_col="SampleID", cohort_col="Cohort")

Citation

HIDE-deconv's deconvolution algorithm is based on HIDE: Hierarchical Cell Type Deconvolution. If you use HIDE-deconv, please cite the following article.

Dennis Völkl, Malte Mensching-Buhr, Thomas Sterr, Sarah Bolz, Andreas Schäfer, Nicole Seifert, Jana Tauschke, Austin Rayford, Oddbjørn Straume, Helena U Zacharias, Sushma Nagaraja Grellscheid, Tim Beissbarth, Michael Altenbuchinger, Franziska Görtler, HIDE: hierarchical cell-type deconvolution, Bioinformatics, Volume 41, Issue Supplement_1, July 2025, Pages i207–i216, https://doi.org/10.1093/bioinformatics/btaf179

License

This project is licensed under the MIT License.

Contact

For questions, support or scientific collaboration:

• Dennis Voelkl: dennis.k.voelkl(at)uib.no
• Franziska Goertler: Franziska.Gortler(at)uib.no