Powered by OpenAIRE graph
Found an issue? Give us feedback
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
Bioinformatics
Article
License: CC BY
Data sources: UnpayWall
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
Bioinformatics
Article . 2019 . Peer-reviewed
License: CC BY
Data sources: Crossref
versions View all 2 versions
addClaim

This Research product is the result of merged Research products in OpenAIRE.

You have already added 0 works in your ORCID record related to the merged Research product.

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis

Authors: Vivek Bhardwaj; Steffen Heyne; Katarzyna Sikora; Leily Rabbani; Michael Rauer; Fabian Kilpert; Andreas S. Richter; +2 Authors

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis

Abstract

Abstract Summary Due to the rapidly increasing scale and diversity of epigenomic data, modular and scalable analysis workflows are of wide interest. Here we present snakePipes, a workflow package for processing and downstream analysis of data from common epigenomic assays: ChIP-seq, RNA-seq, Bisulfite-seq, ATAC-seq, Hi-C and single-cell RNA-seq. snakePipes enables users to assemble variants of each workflow and to easily install and upgrade the underlying tools, via its simple command-line wrappers and yaml files. Availability and implementation snakePipes can be installed via conda: `conda install -c mpi-ie -c bioconda -c conda-forge snakePipes’. Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online. Supplementary information Supplementary data are available at Bioinformatics online.

Subjects by Vocabulary

Microsoft Academic Graph classification: Downstream (software development) Computer science RNA-Seq computer.software_genre Exome sequencing Epigenomics Scalability Operating system computer

Keywords

Epigenomics, Statistics and Probability, Biochemistry, Workflow, Exome Sequencing, RNA-Seq, Molecular Biology, Genome Analysis, Applications Notes, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, Software

12 references, page 1 of 2

Danecek P.et al (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156–2158.21653522 [OpenAIRE] [PubMed]

Di Tommaso P.et al (2017) Nextflow enables reproducible computational workflows. Nat. Biotechnol., 35, 316–319.28398311 [OpenAIRE] [PubMed]

Ewels P.et al (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32, 3047–3048.27312411 [OpenAIRE] [PubMed]

Giorgetti L.et al (2016) Structural organization of the inactive X chromosome in the mouse. Nature, 535, 575–579.27437574 [OpenAIRE] [PubMed]

Goecks J.et al (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.20738864 [OpenAIRE] [PubMed]

Grüning B.et al (2018) Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat. Methods, 15, 475–476.29967506 [OpenAIRE] [PubMed]

Köster J., Rahmann S. (2012) Snakemake–a scalable bioinformatics workflow engine. Bioinformatics, 28, 2520–2522.22908215 [OpenAIRE] [PubMed]

Krueger F., Andrews S.R. (2016) SNPsplit: allele-specific splitting of alignments between genomes with known SNP genotypes. F1000Res., 5, 1479.27429743 [OpenAIRE] [PubMed]

Lea A.J.et al (2018) Genome-wide quantification of the effects of DNA methylation on human gene regulation. Elife, 7, e37513.30575519 [OpenAIRE] [PubMed]

Ramírez F.et al (2018) High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nat. Commun., 9, 189.29335486 [OpenAIRE] [PubMed]

  • BIP!
    Impact byBIP!
    citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    109
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 1%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Top 10%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 1%
  • citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    109
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 1%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Top 10%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 1%
    Powered byBIP!BIP!
Powered by OpenAIRE graph
Found an issue? Give us feedback
citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
109
Top 1%
Top 10%
Top 1%
Green
hybrid