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sinclair

scRNASeq pipeline

https://github.com/ccbr/sinclair

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 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

scRNASeq pipeline

Basic Info
Statistics
  • Stars: 1
  • Watchers: 8
  • Forks: 3
  • Open Issues: 48
  • Releases: 7
Created almost 3 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

SINCLAIR

SINgle CelL AnalysIs Resource

build docs DOI release

View the documentation here: https://ccbr.github.io/SINCLAIR/

Introduction

SINCLAIR was developed by the CCR Collaborative Bioinformatics Resource as an open-source, reproducible solution for multiple single cell next-generation modalities. It has been developed solely on Biowulf using Nextflow.

Overview

The pipeline currently begins with either sample FASTQ file or h5 Aligned reads, completing per sample quality control, and per-contrast integration. Quality control reports are generated, as are per-contrast integration reports.

Single cell RNA-Seq GEX pipeline Overview of Single Cell RNASeq Gene Expression Pipeline

Quickstart

SINCLAIR is available on biowulf with the ccbrpipeliner module as of release 8. You can load it on an interactive node with:

sh module load ccbrpipeliner/8

sh sinclair --help sinclair --version

Example usage

1. Initialize your project

--output is optional and defaults to your current working directory.

sh sinclair init --output /path/to/output/dir

2. Update the config files as needed

can change whether cellranger is deployed, species, names of manifest files (default locations listed below)

In /path/to/output/dir:

  • assets/params.yml
  • assets/input_manifest.csv
  • assets/contrast_manifest.csv
3. Run the pipeline

A) preview without executing

sh sinclair run -preview --output /path/to/output/dir -params-file assets/params.yml

B) local run

sh sinclair run --output /path/to/output/dir -params-file assets/params.yml

C) submit to slurm

sh sinclair run --mode slurm --output /path/to/output/dir -params-file assets/params.yml

Help & Contributing

Come across a bug? Open an issue and include a minimal reproducible example.

Have a question? Ask it in discussions.

Want to contribute to this project? Check out the contributing guidelines.

General Inquiries and Collaboration: Please contact the CCBR Pipeliner team at CCBR_Pipeliner@mail.nih.gov.

Owner

  • Name: CCR Collaborative Bioinformatics Resource
  • Login: CCBR
  • Kind: organization
  • Email: nciccbr@mail.nih.gov
  • Location: United States of America

CCR Collaborative Bioinformatics Resource, Center for Cancer Research (NCI), National Institutes of Health

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "Please cite SINCLAIR as below:"
authors:
  - family-names: Sevilla
    given-names: Samantha
    orcid: https://orcid.org/0000-0002-8734-9875
    affiliation:
      Advanced Biomedical Computational Science, Frederick National Laboratory
      for Cancer Research, Frederick, MD 21702, USA
  - family-names: Wong
    given-names: Nathan
    orcid: https://orcid.org/0000-0002-8882-3401
    affiliation:
      Advanced Biomedical Computational Science, Frederick National Laboratory
      for Cancer Research, Frederick, MD 21702, USA
  - family-names: Sovacool
    given-names: Kelly
    orcid: https://orcid.org/0000-0003-3283-829X
    affiliation:
      Advanced Biomedical Computational Science, Frederick National Laboratory
      for Cancer Research, Frederick, MD 21702, USA
  - family-names: Pehrsson
    given-names: Erica
    orcid: https://orcid.org/0000-0002-2968-6179
    affiliation:
      Advanced Biomedical Computational Science, Frederick National Laboratory
      for Cancer Research, Frederick, MD 21702, USA
  - family-names: Abdelmaksoud
    given-names: Abdalla
  - family-names: Koparde
    given-names: Vishal
    orcid: https://orcid.org/0000-0001-8978-8495
    affiliation:
      Advanced Biomedical Computational Science, Frederick National Laboratory
      for Cancer Research, Frederick, MD 21702, USA
title: "SINCLAIR: SINgle CelL AnalysIs Resource"
url: https://ccbr.github.io/SINCLAIR
repository-code: https://github.com/CCBR/SINCLAIR
license: MIT
type: software
identifiers:
  - description: Archived snapshots of all versions
    type: doi
    value: 10.5281/zenodo.15283503
version: v0.3.4
date-released: "2025-08-22"

GitHub Events

Total
  • Create event: 43
  • Release event: 2
  • Issues event: 65
  • Watch event: 1
  • Delete event: 38
  • Issue comment event: 44
  • Push event: 190
  • Pull request review comment event: 19
  • Pull request review event: 24
  • Pull request event: 51
  • Fork event: 3
Last Year
  • Create event: 43
  • Release event: 2
  • Issues event: 65
  • Watch event: 1
  • Delete event: 38
  • Issue comment event: 44
  • Push event: 190
  • Pull request review comment event: 19
  • Pull request review event: 24
  • Pull request event: 51
  • Fork event: 3

Dependencies

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