Software Open Access

PEAKachu: a peak calling tool for CLIP/RIP-seq data

Bischler, Thorsten; Förstner, Konrad U.; Maticzka, Daniel; Wright, Patrick R.


JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/98c4c0eb-eceb-43ab-b14d-98478b5e1fac/tbischler/PEAKachu-v0.2.0.zip"
      }, 
      "checksum": "md5:e31d9d9998455ecea3277f02e9346212", 
      "bucket": "98c4c0eb-eceb-43ab-b14d-98478b5e1fac", 
      "key": "tbischler/PEAKachu-v0.2.0.zip", 
      "type": "zip", 
      "size": 4109149
    }
  ], 
  "owners": [
    21282
  ], 
  "doi": "10.5281/zenodo.4669966", 
  "stats": {
    "version_unique_downloads": 2.0, 
    "unique_views": 119.0, 
    "views": 125.0, 
    "version_views": 125.0, 
    "unique_downloads": 2.0, 
    "version_unique_views": 119.0, 
    "volume": 8218298.0, 
    "version_downloads": 2.0, 
    "downloads": 2.0, 
    "version_volume": 8218298.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.4669966", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.4669965", 
    "bucket": "https://zenodo.org/api/files/98c4c0eb-eceb-43ab-b14d-98478b5e1fac", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.4669965.svg", 
    "html": "https://zenodo.org/record/4669966", 
    "latest_html": "https://zenodo.org/record/4669966", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.4669966.svg", 
    "latest": "https://zenodo.org/api/records/4669966"
  }, 
  "conceptdoi": "10.5281/zenodo.4669965", 
  "created": "2021-04-07T13:02:52.902150+00:00", 
  "updated": "2021-04-09T00:27:25.419076+00:00", 
  "conceptrecid": "4669965", 
  "revision": 4, 
  "id": 4669966, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.4669966", 
    "description": "<p>PEAKachu is a peak calling tool for CLIP/RIP-seq data that can be used to identify targets and interaction sites of RNA-binding proteins. The tool is written in Python 3 and depends on several software packages for Python and R.</p>", 
    "license": {
      "id": "ISC"
    }, 
    "title": "PEAKachu: a peak calling tool for CLIP/RIP-seq data", 
    "notes": "The following dependency package versions have been used for PEAKachu v.0.2.0:\nPython: Cython 0.29.13, numpy 1.18.5, scipy 1.3.1, matplotlib 3.3.1, pandas 0.25.1, biopython 1.77, pysam 0.16.0.1, bcbio-gff 0.6.6, statsmodels 0.10.1, numexpr 2.7.0, rpy2 3.1.0\nR: edgeR 3.26.5, DESeq2 1.24.0", 
    "relations": {
      "version": [
        {
          "count": 1, 
          "index": 0, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "4669965"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "4669966"
          }
        }
      ]
    }, 
    "version": "v0.2.0", 
    "keywords": [
      "Peak calling", 
      "CLIP-seq", 
      "RIP-seq"
    ], 
    "publication_date": "2021-04-07", 
    "creators": [
      {
        "orcid": "0000-0001-9288-9481", 
        "affiliation": "University of Wuerzburg", 
        "name": "Bischler, Thorsten"
      }, 
      {
        "orcid": "0000-0002-1481-2996", 
        "affiliation": "ZB MED", 
        "name": "F\u00f6rstner, Konrad U."
      }, 
      {
        "name": "Maticzka, Daniel"
      }, 
      {
        "name": "Wright, Patrick R."
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "software", 
      "title": "Software"
    }, 
    "related_identifiers": [
      {
        "scheme": "url", 
        "identifier": "https://github.com/tbischler/PEAKachu/tree/v0.2.0", 
        "relation": "isSupplementTo"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.4669965", 
        "relation": "isVersionOf"
      }
    ]
  }
}
125
2
views
downloads
All versions This version
Views 125125
Downloads 22
Data volume 8.2 MB8.2 MB
Unique views 119119
Unique downloads 22

Share

Cite as