Data

Tools

Indexes

Applications

Experiments

Open Source Science

futuriandge

This is a personal project focused on creating uniformal pipeline for processing RNA-seq data with the end goal to create a .Rdata object which can be imported into R/Shiny app for downstream analysis and hypothesis testing.

https://github.com/ajandria/futuriandge

Science Score: 18.0%

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
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.9%) to scientific vocabulary

Keywords

differential-expression nextflow nextflow-dsl2 pipeline rna-seq
Last synced: 6 months ago · JSON representation ·

Repository

This is a personal project focused on creating uniformal pipeline for processing RNA-seq data with the end goal to create a .Rdata object which can be imported into R/Shiny app for downstream analysis and hypothesis testing.

Basic Info
  • Host: GitHub
  • Owner: ajandria
  • License: bsd-4-clause
  • Language: Groovy
  • Default Branch: main
  • Homepage:
  • Size: 2.86 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Topics
differential-expression nextflow nextflow-dsl2 pipeline rna-seq
Created about 3 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License Code of conduct Citation

README.Md

Nextflow run with conda run with docker run with singularity

Introduction

Welcome to DERNA-Seqnf - a bioinformatics best-practice analysis pipeline for up-stream processing of RNA-Seq data with the main focus on differential expression analysis.

Run test data as:

nextflow run ajandria/futuriandge -r main -latest -profile cluster,conda,test --organism mouse --outDir .

Standard pipeline run:

nextflow run ajandria/futuriandge -r main -latest -profile cluster,singularity --organism mouse/human --outDir . --input samplesheet.csv

Currently the pipeline supports only the MUB infrastructure (hardcoded references).

Owner

  • Name: Adrian
  • Login: ajandria
  • Kind: user
  • Location: Poland

Citation (CITATIONS.md) 

# nf-core/futuriandge: 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

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

- [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.

## 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)

- [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
Last Year

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 12
  • Average time to close issues: about 2 months
  • Average time to close pull requests: less than a minute
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.08
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ajandria (1)
Pull Request Authors
  • ajandria (12)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

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