spatialvi

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

https://github.com/nf-core/spatialvi

Science Score: 57.0%

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

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 10 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (11.5%) to scientific vocabulary

Keywords

10x-genomics 10xgenomics bioinformatics image-processing microscopy nextflow nf-core pipeline rna-seq single-cell spatial spatial-transcriptomics st transcriptomics visium workflow

Last synced: 6 months ago · JSON representation ·

Repository

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Basic Info

Host: GitHub
Owner: nf-core
License: mit
Language: Nextflow
Default Branch: dev
Homepage: https://nf-co.re/spatialvi
Size: 7.11 MB

Statistics

Stars: 65
Watchers: 172
Forks: 25
Open Issues: 7
Releases: 0

Topics

10x-genomics 10xgenomics bioinformatics image-processing microscopy nextflow nf-core pipeline rna-seq single-cell spatial spatial-transcriptomics st transcriptomics visium workflow

Created almost 4 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

Introduction

nf-core/spatialvi is a bioinformatics analysis pipeline for Visium spatial transcriptomics data from 10x Genomics. It can process and analyse spatial data either directly from raw data by running Space Ranger or data already processed by Space Ranger. The pipeline currently consists of the following steps:

Spatialvi Workflow

Raw data processing with Space Ranger (optional)
Quality controls and filtering
Normalisation
Dimensionality reduction and clustering
Differential gene expression testing

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website.

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

You can run the pipeline using:

bash nextflow run nf-core/spatialvi \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/spatialvi was originally developed by the Jackson Laboratory¹, up to the 0.1.0 tag. It was further developed in a collaboration between the National Bioinformatics Infrastructure Sweden and National Genomics Infrastructure within SciLifeLab; it is currently developed and maintained by Erik Fasterius and Christophe Avenel.

Many thanks to others who have helped out along the way too, especially Gregor Sturm!

¹ Supported by grants from the US National Institutes of Health U24CA224067 and U54AG075941. Original authors Dr. Sergii Domanskyi, Prof. Jeffrey Chuang and Dr. Anuj Srivastava.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #spatialvi channel (you can join with this invite).

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Owner

Name: nf-core
Login: nf-core
Kind: organization
Email: core@nf-co.re

Website: http://nf-co.re
Twitter: nf_core
Repositories: 84
Profile: https://github.com/nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md)

# nf-core/spatialvi: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [AnnData](https://github.com/scverse/anndata)

  > Virshup I, Rybakov S, Theis FJ, Angerer P, Wolf FA. bioRxiv 2021.12.16.473007; doi: https://doi.org/10.1101/2021.12.16.473007

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [Quarto](https://quarto.org/)

  > Allaire J, Teague C, Scheidegger C, Xie Y, Dervieux C. Quarto (2022). doi: 10.5281/zenodo.5960048

- [Scanpy](https://github.com/theislab/scanpy)

  > Wolf F, Angerer P, Theis F. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol 19, 15 (2018). doi: https://doi.org/10.1186/s13059-017-1382-0

- [Space Ranger](https://www.10xgenomics.com/support/software/space-ranger)

  > 10x Genomics Space Ranger 2.1.0 [Online]

- [SpatialData](https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1)

  > Marconato L, Palla G, Yamauchi K, Virshup I, Heidari E, Treis T, Toth M, Shrestha R, Vöhringer H, Huber W, Gerstung M, Moore J, Theis F, Stegle O. SpatialData: an open and universal data framework for spatial omics. bioRxiv 2023.05.05.539647; doi: https://doi.org/10.1101/2023.05.05.539647

- [Squipy](https://www.nature.com/articles/s41592-021-01358-2)

  > Palla G, Spitzer H, Klein M et al. Squidpy: a scalable framework for spatial omics analysis. Nat Methods 19, 171–178 (2022). doi: https://doi.org/10.1038/s41592-021-01358-2

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total

Issues event: 9
Watch event: 8
Delete event: 14
Issue comment event: 38
Push event: 67
Pull request review comment event: 4
Pull request review event: 10
Pull request event: 33
Fork event: 5
Create event: 17

Last Year

Issues event: 9
Watch event: 8
Delete event: 14
Issue comment event: 38
Push event: 67
Pull request review comment event: 4
Pull request review event: 10
Pull request event: 33
Fork event: 5
Create event: 17

Committers

Last synced: over 1 year ago

All Time

Total Commits: 542
Total Committers: 13
Avg Commits per committer: 41.692
Development Distribution Score (DDS): 0.347

Past Year

Commits: 237
Committers: 6
Avg Commits per committer: 39.5
Development Distribution Score (DDS): 0.173

Top Committers

Name	Email	Commits
Erik Fasterius	e**s@o**m	354
Gregor Sturm	g**m@b**m	78
Christophe Avenel	c**l@i**e	42
Sergii Domanskyi	s**i@j**g	34
nf-core-bot	c**e@n**e	19
Gregor Sturm	m**l@g**e	4
Sergii Domanskyi	s**i@g**m	3
Christophe Avenel	c**2@I**e	2
Alexander Peltzer	a****r	2
Christophe Avenel	c**l@r**e	1
Christophe Avenel	c**l@r**e	1
Sergii Domanskyi	d**s@s**g	1
domans	d**s@s**2	1

Committer Domains (Top 20 + Academic)

sumner043.sumner.jax.org: 1 rackham3.uppmax.uu.se: 1 rackham2.uppmax.uu.se: 1 it-wl-chrav452.user.uu.se: 1 gregor-sturm.de: 1 nf-co.re: 1 jax.org: 1 it.uu.se: 1 boehringer-ingelheim.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 3
Total pull requests: 12
Average time to close issues: 4 months
Average time to close pull requests: 9 days
Total issue authors: 3
Total pull request authors: 2
Average comments per issue: 0.67
Average comments per pull request: 0.5
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 12
Average time to close issues: 4 months
Average time to close pull requests: 9 days
Issue authors: 3
Pull request authors: 2
Average comments per issue: 0.67
Average comments per pull request: 0.5
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

fasterius (3)
pstorozenko (1)
gboscagli (1)
Alan-pad (1)
aguang (1)
LucFrancisENX (1)
Chrisdoan9 (1)
grst (1)

Pull Request Authors

fasterius (17)
nf-core-bot (11)
cavenel (3)

Top Labels

Issue Labels

bug (4) enhancement (4) documentation (1)

Pull Request Labels

Dependencies

.github/workflows/awsfulltest.yml actions

nf-core/tower-action v2 composite

.github/workflows/awstest.yml actions

nf-core/tower-action v2 composite

.github/workflows/branch.yml actions

mshick/add-pr-comment v1 composite

.github/workflows/ci.yml actions

actions/checkout v2 composite

.github/workflows/linting.yml actions

actions/checkout v2 composite
actions/checkout v1 composite
actions/setup-node v1 composite
actions/setup-python v1 composite
actions/upload-artifact v2 composite
mshick/add-pr-comment v1 composite

.github/workflows/linting_comment.yml actions

dawidd6/action-download-artifact v2 composite
marocchino/sticky-pull-request-comment v2 composite

.github/workflows/clean-up.yml actions

actions/stale v7 composite

.github/workflows/fix-linting.yml actions

actions/checkout v3 composite
actions/setup-node v3 composite

modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan

modules/nf-core/fastqc/meta.yml cpan

modules/nf-core/multiqc/meta.yml cpan

modules/nf-core/spaceranger/count/meta.yml cpan

modules/nf-core/untar/meta.yml cpan

env/reports/Dockerfile docker

condaforge/mambaforge 23.1.0-1 build
jdutant/quarto-minimal 1.3.313 build

pyproject.toml pypi

.github/workflows/release-announcements.yml actions

actions/setup-python v4 composite
rzr/fediverse-action master composite
zentered/bluesky-post-action v0.0.2 composite

.github/workflows/download_pipeline.yml actions

actions/setup-python v5 composite
eWaterCycle/setup-singularity v7 composite
nf-core/setup-nextflow v1 composite

modules/nf-core/custom/dumpsoftwareversions/environment.yml conda

multiqc 1.19.*

modules/nf-core/fastqc/environment.yml conda

fastqc 0.12.1.*

modules/nf-core/multiqc/environment.yml conda

multiqc 1.19.*

modules/nf-core/untar/environment.yml conda

grep 3.11.*
sed 4.7.*
tar 1.34.*

env/reports/environment.yml pypi

SpatialDE ==1.1.3

env/st_spatial_de/environment.yml pypi

SpatialDE ==1.1.3

spatialvi

Science Score: 57.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Introduction

Usage

Pipeline output

Credits

Contributions and Support

Citations

Owner

Citation (CITATIONS.md)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies