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scflow

Documentation Status

This repository contains a collection of pipelines that aid the analysis of single cell sequencing experiments. Currently there is one pipeline implimented that allows the analysis of drop-seq and 10X sequencing analysis. Current pipelines in development: 1) pseudoalignment scpipeline 2) velocyto pipeline 2) kallisto bustools pipeline.

Installation

Conda installation - in progress

The preferred method for installation is through conda/mamba. Preferably the installation should be in a seperate environment::

mamba env create -f conda/environments/scflow.yml
conda activate scflow
python setup.py develop

# Install a specific version of kb-tools from Adam's cloned repo
git clone git@github.com:Acribbs/kb_python.git
cd kb_python
python setup.py develop

scflow --help

Usage

Run the scflow --help command view the help documentation for how to run the single-cell repository.

To run the main single_cell droplet based pipeline run first generate a configuration file::

scflow singlecell config

Then run the pipeline::

scflow singlecell make full -v5

Then to run the report::

scflow singlecell make build_report

Documentation

Further help that introduces single-cell and provides a tutorial of how to run example code can be found at read the docs

Pipelines overview

scflow main quantnuclei

scflow main quantcells

seurat qc-1

seurat filter-2

seurat cluster-3

seurat doublet-4

seurat integration-5

Project Info