sincei 0.2

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.

• Documentation:
• Source code:

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:

cd <your_programs_folder>
conda create -n sincei -c conda-forge -c bioconda scanpy deeptools
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

Full Documentation.