cell2sentence 0.0.1

cell2sentence: create cell sentences from sequencing data

cell2sentence

Reframing cells as sentences of genes, ordered by expression. Please read the manuscript on bioRxiv for methodological details and examples.

(https://www.biorxiv.org/content/10.1101/2022.09.18.508438)

Stable Setup

Install cell2sentence from PyPI with

pip install cell2sentence

Convert Anndata Object to Cell Sentences

After your data is loaded into a standard AnnData adata object, you may create a cell2sentence object with:

import cell2sentence as cs

csdata = cs.transforms.csdata_from_adata(adata)

and generate a list of cell sentences with:

sentences = csdata.create_sentence_lists()

A tutorial script showing how to use pretrained word vectors to analyze the pbmc3k dataset used by Seurat and scanpy in their guided clustering tutorials is available at tutorials/pbmc3k_cell_sentences.py

Development Setup

Create a conda environment using python3 using anaconda with:

conda create -n cell2sentence python=3.8

and activate the environment with

conda activate cell2sentence

finally, you can install the latest development version of cell2sentence by running

make install

which simply uses pip -e.

Loading Data

All data used in the bioRxiv manuscript are publicly available, and details are outlined in the DATA.md file in this repository.