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- Vivek Bhardwaj
- Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany
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- Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany
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- Katarzyna Sikora
- Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany
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- Leily Rabbani
- Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany
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- Michael Rauer
- Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany
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- Fabian Kilpert
- Institutes of Neurogenetics & Cardiogenetics, University of Lübeck , 23562 Lübeck, Germany
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- Andreas S Richter
- Genedata AG , 4053 Basel, Switzerland
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- Devon P Ryan
- Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany
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- Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany
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- Bonnie Berger
- editor
説明
<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Summary</jats:title> <jats:p>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.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>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.</jats:p> </jats:sec> <jats:sec> <jats:title>Supplementary information</jats:title> <jats:p>Supplementary data are available at Bioinformatics online.</jats:p> </jats:sec>
収録刊行物
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- Bioinformatics
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Bioinformatics 35 (22), 4757-4759, 2019-05-27
Oxford University Press (OUP)