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.

You can install scflow using pip, this will only install the package without any dependancies, which will have to be installed seperately.::

pip install scflow

The preferred method for installation is through conda. Currently this installation is still in working progress. Preferably the installation should be in a seperate environment::

conda create -n scflow -c cgat scflow
conda activate scflow
scflow --help

The repository can also be installed manually, but dependencies will need to be installed seperately::

python setup.py install
scflow --help

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

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

• Introduction to the quantnuclei pipeline

• Overview of the quantnuclei pipeline

• Introduction to the quantcells pipeline

• Overview of the seurat qc-1 pipeline

• Overview of the seurat filter-2 pipeline

• Overview of the seurat cluster-3 pipeline

• Overview of the seurat doublet-4 pipeline

• Contributors

• License

• How to contribute