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Tangerine (Transcription Factor Accessibility Network and Gene Expression Regulation) is a tool to quantify the effect of transcription factor binding on gene regulation.

Install

Clone the repository and install with poetry by running these commands

conda config --add channels bioconda
conda config --add channels conda-forge
conda create -n tang python=3.10 scanpy python-igraph leidenalg typer poetry pysam=0.22 bioconda::htseq conda-forge::pyarrow

pip install dash gimmemotifs --no-cache-dir
conda install dash-bootstrap-components
poetry install --only-root

Install the genome of your choice. For example, let's install the mm10 genome.

genomepy install mm10 --provider UCSC --annotation

Quick start

Tangerine assumes that your single cell longitudinal data is already available as an AnnData object, with the adata.obs having an additional column indicating the time of sampling of the cell.

There are two steps to the pipeline -

1. Process the data to estimate TF-TF and TF-gene regulation
2. Inspect the regulatory relationships using an interactive visualisation

Preprocess data

tangerine process \
    -ap path/to/adata \
    -g reference_genome \
    -t "name of time column in adata.obs" \
    -tp "list of time points" \
    -sw "length of scan window in bp" \
    -sp path/to/save/results

Visualise

tangerine visualise \
    -tp "list of time points" \
    -sp path/to/saved/results

Bug Reports and Suggestions for Improvement

Please raise an issue if you find bugs or if you have any suggestions for improvement.