sincei 0.3

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.

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 sincei

For the latest development version, try:

(sincei): pip install 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 -i groupinfo.txt -o coverage