sincei 0.4

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

Please browse the full documentation for tutorials on how to use sincei on 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.

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.