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cell-seek

One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.

https://github.com/openomics/cell-seek

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 10 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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  • ○
    Scientific vocabulary similarity
    Low similarity (15.0%) to scientific vocabulary

Keywords

10xgenomics single-cell-atac-seq single-cell-cite-seq single-cell-omics single-cell-rna-seq single-cell-vdj
Last synced: 10 months ago · JSON representation ·

Repository

One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.

Basic Info
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 9
Topics
10xgenomics single-cell-atac-seq single-cell-cite-seq single-cell-omics single-cell-rna-seq single-cell-vdj
Created about 3 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License Citation

README.md

cell-seek 🔬

**_One single-cell pipeline to rule them all!_** [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10181524.svg)](https://doi.org/10.5281/zenodo.10181524) [![GitHub release (latest SemVer including pre-releases)](https://img.shields.io/github/v/release/OpenOmics/cell-seek?color=blue&include_prereleases)](https://github.com/OpenOmics/cell-seek/releases) [![Docker Pulls](https://img.shields.io/docker/pulls/skchronicles/chicyte)](https://hub.docker.com/repository/docker/skchronicles/chicyte)
[![tests](https://github.com/OpenOmics/cell-seek/workflows/tests/badge.svg)](https://github.com/OpenOmics/cell-seek/actions/workflows/main.yaml) [![docs](https://github.com/OpenOmics/cell-seek/workflows/docs/badge.svg)](https://github.com/OpenOmics/cell-seek/actions/workflows/docs.yml) [![GitHub issues](https://img.shields.io/github/issues/OpenOmics/cell-seek?color=brightgreen)](https://github.com/OpenOmics/cell-seek/issues) [![GitHub license](https://img.shields.io/github/license/OpenOmics/cell-seek)](https://github.com/OpenOmics/cell-seek/blob/main/LICENSE) This is the home of the pipeline, cell-seek. Its long-term goals: to accurately process and analyze single cell data like no pipeline before!

Overview

Welcome to cell-seek! Before getting started, we highly recommend reading through cell-seek's documentation.

The ./cell-seek pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:

cell-seek is a comprehensive set of pipelines to perform the initial processing of different single cell technologies. It relies on technologies like Singularity1 to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by Snakemake2, a flexible and scalable workflow management system, to submit jobs to a cluster.

The pipeline is compatible with data generated from Illumina short-read sequencing technologies. As input, it accepts a set of FastQ files and can be run locally on a compute instance or on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users.

Before getting started, we highly recommend reading through the usage section of each available sub command.

For more information about issues or trouble-shooting a problem, please checkout our FAQ prior to opening an issue on Github.

Dependencies

Requires: singularity>=3.5 snakemake>=6.0

At the current moment, the pipeline uses a mixture of enviroment modules and docker images; however, this will be changing soon! In the very near future, the pipeline will only use docker images. With that being said, snakemake and singularity must be installed on the target system. Snakemake orchestrates the execution of each step in the pipeline. To guarantee the highest level of reproducibility, each step of the pipeline will rely on versioned images from DockerHub. Snakemake uses singularity to pull these images onto the local filesystem prior to job execution, and as so, snakemake and singularity will be the only two dependencies in the future.

Installation

Please clone this repository to your local filesystem using the following command: ```bash

Clone Repository from Github

git clone https://github.com/OpenOmics/cell-seek.git

Change your working directory

cd cell-seek/

Add dependencies to $PATH

Biowulf users should run

module load snakemake singularity

Get usage information

./cell-seek -h ```

Contribute

This site is a living document, created for and by members like you. cell-seek is maintained by the members of OpenOmics and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our GitHub repository.

Cite

If you use this software, please cite it as below:

@BibText ```text @software{Chen_Kuhn_OpenOmics_cell-seek_2023, author = {Vicky Chen and Skyler Kuhn}, title = {OpenOmics/cell-seek}, month = nov, year = 2023, publisher = {Zenodo}, doi = {10.5281/zenodo.10181524}, url = {https://doi.org/10.5281/zenodo.10181524} } ```
@APA ```text Vicky Chen, & Skyler Kuhn. (2023). OpenOmics/cell-seek [Computer software]. https://doi.org/10.5281/zenodo.10181524 ```

For more citation style options, please visit the pipeline's Zenodo page.

References

1. Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.
2. Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.

Owner

  • Name: OpenOmics
  • Login: OpenOmics
  • Kind: organization
  • Location: United States of America

Open Bioinformatics Research

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Chen
    given-names: Vicky
    orcid: https://orcid.org/0000-0003-4595-154X
  - family-names: Kuhn
    given-names: Skyler
    orcid: https://orcid.org/0000-0003-0606-2125
title: OpenOmics/cell-seek
doi: 10.5281/zenodo.10181524
date-released: 2023-11-21
url: "https://github.com/OpenOmics/cell-seek/"

GitHub Events

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  • Pull request review event: 2
  • Pull request event: 8
Last Year
  • Create event: 10
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  • Issue comment event: 5
  • Member event: 1
  • Push event: 38
  • Pull request review event: 2
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Issues and Pull Requests

Last synced: 10 months ago

All Time
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  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.0
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  • Bot issues: 0
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Past Year
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  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 days
  • Issue authors: 1
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  • Average comments per issue: 0.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
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  • rroutsong (1)
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Dependencies

.github/workflows/docs.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/main.yaml actions
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  • docker://snakemake/snakemake v5.24.2 composite
docs/requirements.txt pypi
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  • importlib-metadata >=3.10
  • joblib ==0.16.0
  • jsmin ==3.0.0
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  • nltk >=3.6.6
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  • pymdown-extensions *
  • pytz ==2020.1
  • regex *
  • six ==1.15.0
  • smmap ==3.0.4
  • tornado ==6.0.4
  • tqdm ==4.48.2
  • zipp ==3.1.0