Knowledge base

Introduction of Sushi package

Introduction

Sushi package can draw a variety of common genome formats, including bed, bedpe, bedgraph, Hic matrix, Manhattan map, gene structure map.

Code explanation

For the convenience of searching this time, I divided them into different articles. The cover of each article is the corresponding rendering.

  1. bedgraph

    http://54.189.29.251/2020/09/04/%e7%bb%98%e5%88%b6bedgraph%e6%a0%bc%e5%bc%8f%e5%9b%be/
  2. multiple bedgraph

    http://54.189.29.251/2020/09/04/%e7%bb%98%e5%88%b6bedgraph%e6%a0%bc%e5%bc%8f%e5%9b%be/
  3. HiC interaction matrix

    http://www.thecodesearch.com/2020/09/06/%e7%bb%98%e5%88%b6hic%e4%ba%a4%e4%ba%92%e5%9b%be/
  4. Bedpe format


    http://www.thecodesearch.com/2020/09/09/sushi%e5%8c%85%e7%bb%98%e5%88%b6bedpe%e5%9b%be/
  5. bed format

    http://www.thecodesearch.com/2020/09/09/sushi%e5%8c%85%e7%bb%98%e5%88%b6bed%e5%9b%be/
  6. Manhattan figure

    http://www.thecodesearch.com/2020/09/13/sushi%e5%8c%85%e7%bb%98%e5%88%b6manhattan%e5%9b%be/
  7. gene stucture figure

    http://www.thecodesearch.com/2020/09/13/sushi%e5%8c%85%e7%bb%98%e5%88%b6%e5%9f%ba%e5%9b%a0%e7%bb%93%e6%9e%84%e5%9b%be/
  8. Enlarge part of the image

    http://www.thecodesearch.com/2020/09/13/sushi%e7%bb%98%e5%88%b6%e9%83%a8%e5%88%86%e6%94%be%e5%a4%a7%e7%9a%84bedgraph%e5%9b%be/

    Reference

    https://www.bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf
    https://github.com/DavidQuigley/WCDT_WGBS/blob/master/scripts/2019_05_15_prepare_environment.r

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