sincei: A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data.

Features

sincei provides a flexible, easy-to-use command-line interface to work with single-cell data directly from BAM files. It can:

• Aggregate signal in bins, genes or any feature of interest from single-cells.
• Perform read-level and count-level quality control.
• Perform dimensionality reduction and clustering of all kinds of single-cell data (open chromatin, histone marks, methylation, gene expression etc..).
• Create coverage files (bigwigs) for visualization.

For details, please read our preprint describing sincei.

Full Documentation

Please browse the full documentation for tutorials on how to use sincei on the command line, as well as details of our python API.

Installation

sincei is a command line toolkit based on python3, and can be installed using conda.

The recommended way to install sincei is via bioconda:

conda create -n sincei -c bioconda -c conda-forge sincei

Alternatively, a development version can be installed via GitHub.

conda create -n sincei python=3.8
conda activate sincei
pip install --editable=git+https://github.com/bhardwaj-lab/sincei.git@develop#egg=sincei

Usage

Get the tool list with sincei --help

Each tool begins with the prefix sc<tool_name>, such as:

scBulkCoverage -b file1.bam -g groupinfo.txt -o coverage

Citation

Please cite sincei as: "Bhardwaj V. , Mourragui, S. (2024) User-friendly exploration of epigenomic data in single cells using sincei. biorXiv. doi: 10.1101/2024.07.27.605424"

Questions and discussions

To ask a question related to sincei or start a new discussion, please use our github discussion forum.