sc-samap 3.0.1

The SAMap algorithm

SAMap -- version 3.0.0

Citation

Please cite the following paper if using SAMap: https://elifesciences.org/articles/66747

Tarashansky, Alexander J., et al. "Mapping single-cell atlases throughout Metazoa unravels cell type evolution." Elife 10 (2021): e66747.

Requirements: Python ≥3.11. See pyproject.toml for the full dependency list.

Installation

SAMap requires Python ≥3.11.

From PyPI (recommended)

conda create -n SAMap -c conda-forge python=3.12 pip
conda activate SAMap
pip install sc-samap

From source (development)

conda create -n SAMap -c conda-forge python=3.12 pip
conda activate SAMap
git clone https://github.com/atarashansky/SAMap.git
cd SAMap
pip install -e .

NCBI BLAST

SAMap requires NCBI BLAST on your PATH for the homology mapping step.

Easiest via conda:

conda install -c bioconda blast

Or download binaries directly from NCBI.

Installation time should take no more than 10 minutes.

Running BLAST

The BLAST mapping script can be run from the SAMap_vignette.ipynb Jupyter notebook.

Depending on the number of cores available on your machine and the size/type of the input fasta files, this step may take up to around 4 hours.

Running SAMap

To run SAMap, use the SAMAP class from samap:

from samap import SAMAP
sm = SAMAP(sams={'sp1': 'species1.h5ad', 'sp2': 'species2.h5ad'}, f_maps='maps/')
sm.run()

See the function documentation for a description of the inputs and outputs. Take a look at the provided Jupyter notebook to get started (SAMap_vignette.ipynb).