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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.

tangerine_screen.mp4

Install

Clone the repository

git clone https://github.com/ntanmayee/tangerine.git
cd tangerine

Install tangerine 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

conda activate tang

pip install dash gimmemotifs --no-cache-dir
conda install dash-bootstrap-components
pip install dash-cytoscape==0.2.0
poetry install --only-root

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

genomepy install mm10 --provider UCSC --annotation

You will also need a BED file with the list of genes and their sequence information. It should have chr, start, end and gene_name columns.

Check out the Jupyter Notebook tutorial!

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 \
    -b mm10_genes.bed \
    -m kmeans \
    -dt 50

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.