sincei 0.3.1

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

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 dimentionality reduction and clustering of all kinds of single-cell data (open chromatin, histone marks, methylation, gene expression etc..).
• Create coverage files (bigwigs) for visualization.

Full Documentation

Installation

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

Create a new conda environment and install sincei stable release from github using:

conda create -n sincei -c anaconda python=3.8
conda activate sincei
(sincei): pip install --editable=git+https://github.com/vivekbhr/sincei.git@master#egg=sincei

For the development version, try:

(sincei): pip install --editable=git+https://github.com/vivekbhr/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

Questions and discussions

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