Software Open Access

CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis

Zhu, Qian; Liu, Nan; Orkin, Stuart; Yuan, Guo-Cheng


JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/401f811c-e2b2-4b7f-b20a-7861c7a2469a/cutruntools.tar.gz"
      }, 
      "checksum": "md5:f2758ac7b247f827fe0c745cbeb90c54", 
      "bucket": "401f811c-e2b2-4b7f-b20a-7861c7a2469a", 
      "key": "cutruntools.tar.gz", 
      "type": "gz", 
      "size": 487201
    }
  ], 
  "owners": [
    75210
  ], 
  "doi": "10.5281/zenodo.3374112", 
  "stats": {
    "version_unique_downloads": 1.0, 
    "unique_views": 18.0, 
    "views": 20.0, 
    "downloads": 1.0, 
    "unique_downloads": 1.0, 
    "version_unique_views": 18.0, 
    "volume": 487201.0, 
    "version_downloads": 1.0, 
    "version_views": 20.0, 
    "version_volume": 487201.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.3374112", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.3374111", 
    "bucket": "https://zenodo.org/api/files/401f811c-e2b2-4b7f-b20a-7861c7a2469a", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.3374111.svg", 
    "html": "https://zenodo.org/record/3374112", 
    "latest_html": "https://zenodo.org/record/3374112", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.3374112.svg", 
    "latest": "https://zenodo.org/api/records/3374112"
  }, 
  "conceptdoi": "10.5281/zenodo.3374111", 
  "created": "2019-08-22T06:37:22.731770+00:00", 
  "updated": "2019-08-22T19:06:01.293038+00:00", 
  "conceptrecid": "3374111", 
  "revision": 3, 
  "id": 3374112, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.3374112", 
    "version": "Initial version", 
    "language": "eng", 
    "title": "CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis", 
    "license": {
      "id": "LGPL-2.0-or-later"
    }, 
    "related_identifiers": [
      {
        "scheme": "doi", 
        "identifier": "10.1101/529081", 
        "relation": "cites"
      }, 
      {
        "scheme": "url", 
        "identifier": "https://bitbucket.org/qzhudfci/cutruntools/", 
        "relation": "cites"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.3374111", 
        "relation": "isVersionOf"
      }
    ], 
    "notes": "Please see the repository website http://bitbucket.org/qzhudfci/cutruntools/ for installation and usage information, and for updates. Usage information is also located in this software package. See README.md, INSTALL.md, and USAGE.md for details.", 
    "relations": {
      "version": [
        {
          "count": 1, 
          "index": 0, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "3374111"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "3374112"
          }
        }
      ]
    }, 
    "subjects": [
      {
        "term": "Genomics", 
        "scheme": "url", 
        "identifier": "https://meshb.nlm.nih.gov/record/ui?name=Genomics"
      }, 
      {
        "term": "Computational biology", 
        "scheme": "url", 
        "identifier": "https://meshb.nlm.nih.gov/record/ui?name=Computational%20Biology"
      }, 
      {
        "term": "Software", 
        "scheme": "url", 
        "identifier": "https://meshb.nlm.nih.gov/record/ui?name=Software"
      }, 
      {
        "term": "Chromatin", 
        "scheme": "url", 
        "identifier": "https://meshb.nlm.nih.gov/record/ui?name=Chromatin"
      }, 
      {
        "term": "DNA-binding proteins", 
        "scheme": "url", 
        "identifier": "https://meshb.nlm.nih.gov/record/ui?name=DNA-Binding%20Proteins"
      }, 
      {
        "term": "High-Throughput Nucleotide Sequencing", 
        "scheme": "url", 
        "identifier": "https://meshb.nlm.nih.gov/record/ui?name=High-Throughput%20Nucleotide%20Sequencing"
      }, 
      {
        "term": "Transcription Factors", 
        "scheme": "url", 
        "identifier": "https://meshb.nlm.nih.gov/record/ui?name=Transcription%20Factors"
      }, 
      {
        "term": "DNA Footprinting", 
        "scheme": "url", 
        "identifier": "https://meshb.nlm.nih.gov/record/ui?name=DNA%20Footprinting"
      }
    ], 
    "references": [
      "Zhu et al (2019) bioRxiv 10.1101/529081v1", 
      "Bitbucket repository site: bitbucket.org/qzhudfci/cutruntools/"
    ], 
    "keywords": [
      "protein-DNA binding", 
      "MNase", 
      "transcription factor binding", 
      "chromatin", 
      "high-throughput sequencing", 
      "CUT&RUN", 
      "CUT&Tag", 
      "ATAC-seq", 
      "genomic footprinting"
    ], 
    "publication_date": "2019-08-22", 
    "creators": [
      {
        "affiliation": "Dana Farber Cancer Institute", 
        "name": "Zhu, Qian"
      }, 
      {
        "affiliation": "Boston Children's Hospital", 
        "name": "Liu, Nan"
      }, 
      {
        "affiliation": "Boston Children's Hospital", 
        "name": "Orkin, Stuart"
      }, 
      {
        "affiliation": "Dana Farber Cancer Institute", 
        "name": "Yuan, Guo-Cheng"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "software", 
      "title": "Software"
    }, 
    "description": "<p>We introduce CUT&amp;RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&amp;RUN primary cleavage data. CUT&amp;RUNTools extracts endonuclease cut site information from sequences of short read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&amp;RUN. CUT&amp;RUNTools is available at https://bitbucket.org/qzhudfci/cutruntools/.</p>"
  }
}
20
1
views
downloads
All versions This version
Views 2020
Downloads 11
Data volume 487.2 kB487.2 kB
Unique views 1818
Unique downloads 11

Share

Cite as