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rnadeseq

Differential gene expression analysis and pathway analysis of RNAseq data

https://github.com/qbic-pipelines/rnadeseq

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
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.2%) to scientific vocabulary

Keywords

deseq2 nextflow pathway-analysis pipeline rnaseq
Last synced: 6 months ago · JSON representation ·

Repository

Differential gene expression analysis and pathway analysis of RNAseq data

Basic Info
  • Host: GitHub
  • Owner: qbic-pipelines
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Homepage:
  • Size: 62.5 MB
Statistics
  • Stars: 32
  • Watchers: 3
  • Forks: 23
  • Open Issues: 6
  • Releases: 14
Topics
deseq2 nextflow pathway-analysis pipeline rnaseq
Created over 6 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

qbic-pipelines/rnadeseq

Downstream differential gene expression analysis with DESeq2 package.

Nextflow install with bioconda Docker DOI

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Documentation

The qbic-pipelines/rnadeseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

Credits

qbic-pipelines/rnadeseq was written by Gisela Gabernet (@ggabernet), Silvia Morini (@silviamorins) and Oskar Wacker (@WackerO), at QBiC. The DESeq2 scripts were originally written by @qbicStefanC.

The pipeline structure is based on the template by the nf-core project. For more information, please check out the nf-core website.

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

Owner

  • Name: QBiC (qbic-pipelines)
  • Login: qbic-pipelines
  • Kind: organization
  • Email: support@qbic.zendesk.com
  • Location: University of Tübingen

Bioinformatics analysis pipelines at QBiC

Citation (CITATIONS.md) 

# qbic-pipelines/rnadeseq: 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.

## 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
  • Create event: 4
  • Issues event: 13
  • Release event: 2
  • Delete event: 1
  • Issue comment event: 38
  • Push event: 34
  • Pull request review comment event: 46
  • Pull request review event: 61
  • Pull request event: 37
  • Fork event: 1
Last Year
  • Create event: 4
  • Issues event: 13
  • Release event: 2
  • Delete event: 1
  • Issue comment event: 38
  • Push event: 34
  • Pull request review comment event: 46
  • Pull request review event: 61
  • Pull request event: 37
  • Fork event: 1

Dependencies

environment.yml conda
  • bioconductor-deseq2 1.34.0.*
  • bioconductor-genefilter 1.76.0.*
  • bioconductor-genomeinfodbdata 1.2.7.*
  • bioconductor-impute 1.68.0.*
  • bioconductor-org.hs.eg.db 3.14.0.*
  • bioconductor-org.mm.eg.db 3.14.0.*
  • bioconductor-pathview 1.34.0.*
  • bioconductor-rtracklayer 1.54.0.*
  • bioconductor-summarizedexperiment 1.24.0.*
  • bioconductor-tximeta 1.12.0.*
  • bioconductor-tximport 1.22.0.*
  • bioconductor-vsn 3.62.0.*
  • pandoc 2.17.1.1.*
  • r-base 4.1.2.*
  • r-dplyr 1.0.9.*
  • r-dt 0.20.*
  • r-extrafont 0.17.*
  • r-formattable 0.2.1.*
  • r-ggplot2 3.3.5.*
  • r-gplots 3.1.1.*
  • r-gprofiler2 0.2.1.*
  • r-kableextra 1.3.4.*
  • r-knitr 1.37.*
  • r-optparse 1.7.1.*
  • r-pheatmap 1.0.12.*
  • r-plyr 1.8.6.*
  • r-reshape2 1.4.4.*
  • r-rmarkdown 2.11.*
  • r-svglite 2.1.0.*
  • r-tidyverse 1.3.1.*
  • r-yaml 2.2.2.*
.github/workflows/awsfulltest.yml actions
  • nf-core/tower-action v3 composite
.github/workflows/awstest.yml actions
  • nf-core/tower-action v3 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • Wandalen/wretry.action v1.0.11 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v2 composite
  • nf-core/setup-nextflow v1 composite
  • technote-space/get-diff-action v4 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • mshick/add-pr-comment v1 composite
  • nf-core/setup-nextflow v1 composite
  • psf/black stable composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
.github/workflows/push_dockerhub.yml actions
  • actions/checkout v2 composite
Dockerfile docker
  • condaforge/mambaforge latest build