{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T07:59:50Z","timestamp":1775807990210,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,5,28]],"date-time":"2019-05-28T00:00:00Z","timestamp":1559001600000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Science Foundation","award":["CRC992"],"award-info":[{"award-number":["CRC992"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <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>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>snakePipes can be installed via conda: `conda install -c mpi-ie -c bioconda -c conda-forge snakePipes\u2019. Source code (https:\/\/github.com\/maxplanck-ie\/snakepipes) and documentation (https:\/\/snakepipes.readthedocs.io\/en\/latest\/) are available online.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz436","type":"journal-article","created":{"date-parts":[[2019,5,23]],"date-time":"2019-05-23T07:23:07Z","timestamp":1558596187000},"page":"4757-4759","source":"Crossref","is-referenced-by-count":163,"title":["snakePipes: facilitating flexible, scalable and integrative epigenomic analysis"],"prefix":"10.1093","volume":"35","author":[{"given":"Vivek","family":"Bhardwaj","sequence":"first","affiliation":[{"name":"Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany"},{"name":"Faculty of Biology, University of Freiburg , 79104 Freiburg, Germany"}]},{"given":"Steffen","family":"Heyne","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany"}]},{"given":"Katarzyna","family":"Sikora","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany"}]},{"given":"Leily","family":"Rabbani","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany"}]},{"given":"Michael","family":"Rauer","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany"}]},{"given":"Fabian","family":"Kilpert","sequence":"additional","affiliation":[{"name":"Institutes of Neurogenetics & Cardiogenetics, University of L\u00fcbeck , 23562 L\u00fcbeck, Germany"}]},{"given":"Andreas S","family":"Richter","sequence":"additional","affiliation":[{"name":"Genedata AG , 4053 Basel, Switzerland"}]},{"given":"Devon P","family":"Ryan","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany"}]},{"given":"Thomas","family":"Manke","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Immunobiology and Epigenetics , 79108 Freiburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2019,5,27]]},"reference":[{"key":"2023013108353197300_btz436-B3","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2023013108353197300_btz436-B4","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat. 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