From fd625babd9d55b685600818cca13734b97bc593e Mon Sep 17 00:00:00 2001 From: "action@github.com" Date: Tue, 3 Oct 2023 21:14:21 +0000 Subject: [PATCH] Updates --- 404.html | 4 ++-- about/index.html | 4 ++-- assets/js/{c22a5f69.18d0a96a.js => c22a5f69.98180162.js} | 2 +- .../{runtime~main.aa868d4f.js => runtime~main.5a1d6d55.js} | 2 +- available-data/cgpwgs/index.html | 4 ++-- available-data/pcawg/index.html | 4 ++-- blog/archive/index.html | 4 ++-- blog/first-blog-post/index.html | 4 ++-- blog/index.html | 4 ++-- blog/long-blog-post/index.html | 4 ++-- blog/mdx-blog-post/index.html | 4 ++-- blog/tags/docusaurus/index.html | 4 ++-- blog/tags/facebook/index.html | 4 ++-- blog/tags/hello/index.html | 4 ++-- blog/tags/hola/index.html | 4 ++-- blog/tags/index.html | 4 ++-- blog/welcome/index.html | 4 ++-- category/available-data/index.html | 4 ++-- category/help/index.html | 4 ++-- category/loading-data/index.html | 4 ++-- category/use-cases/index.html | 4 ++-- category/visualizations/index.html | 4 ++-- help/contact/index.html | 4 ++-- help/faq/index.html | 4 ++-- index.html | 4 ++-- intro/index.html | 4 ++-- loading-data/cohort-config-creation/index.html | 4 ++-- loading-data/data-formats/index.html | 4 ++-- loading-data/loading-private-data/index.html | 4 ++-- loading-data/local-data/index.html | 4 ++-- loading-data/python-package/index.html | 4 ++-- loading-data/through-data-config/index.html | 6 +++--- loading-data/through-interface/index.html | 4 ++-- loading-data/thumbnails/index.html | 4 ++-- loading-data/url-parameters/index.html | 4 ++-- markdown-page/index.html | 4 ++-- search/index.html | 4 ++-- use-cases/atm-mutations/index.html | 4 ++-- use-cases/bi-allelic-loss/index.html | 4 ++-- use-cases/brca/index.html | 4 ++-- use-cases/ccne1/index.html | 4 ++-- use-cases/cdk12/index.html | 4 ++-- use-cases/co-amplifications/index.html | 4 ++-- use-cases/global-pattern/index.html | 4 ++-- visualizations/breakpoint-view/index.html | 4 ++-- visualizations/cohort-view/index.html | 4 ++-- visualizations/data-sampling/index.html | 4 ++-- visualizations/export/index.html | 4 ++-- visualizations/genome-view/index.html | 4 ++-- visualizations/navigation/index.html | 4 ++-- visualizations/variant-view/index.html | 4 ++-- workflows/index.html | 4 ++-- 52 files changed, 103 insertions(+), 103 deletions(-) rename assets/js/{c22a5f69.18d0a96a.js => c22a5f69.98180162.js} (73%) rename assets/js/{runtime~main.aa868d4f.js => runtime~main.5a1d6d55.js} (98%) diff --git a/404.html b/404.html index 3f661eba..238acf28 100644 --- a/404.html +++ b/404.html @@ -9,13 +9,13 @@ - +
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Please contact the owner of the site that linked you to the original URL and let them know their link is broken.

- + \ No newline at end of file diff --git a/about/index.html b/about/index.html index af749829..342bb90c 100644 --- a/about/index.html +++ b/about/index.html @@ -9,13 +9,13 @@ - +
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About

Chromoscope is developed and maintained by the members of Department of Biomedical Informatics at Harvard Medical School.

Team​

  • Sehi L'Yi (HiDIVE Lab)
  • Dominika Maziec (Park Lab)
  • Victoria Stevens (Park Lab)
  • Trevor Manz (HiDIVE Lab)
  • Alexander Veit (Park Lab)
  • Michele Berselli (Park Lab)
  • Peter J Park (Park Lab)
  • Dominik Glodzik (Park Lab)
  • Nils Gehlenborg (HiDIVE Lab)

Citation​

When citing Chromoscope in your paper, please cite the following publication.

L'Yi et al. Chromoscope: Interactive Multiscale Visualization for Structural Variation in Human Genomes. OSF Preprints, 10 May 2023. 10.31219/osf.io/pyqrx

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Unique ID.")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"cancer")),(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"string")),(0,r.kt)("td",{parentName:"tr",align:null},"Required. Type of a cancer.")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"assembly")),(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"'hg38'")," or ",(0,r.kt)("inlineCode",{parentName:"td"},"'hg19'")),(0,r.kt)("td",{parentName:"tr",align:null},"Required. Assembly.")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"sv")),(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"string")),(0,r.kt)("td",{parentName:"tr",align:null},"Required. An URL of the SV bedpe file (",(0,r.kt)("inlineCode",{parentName:"td"},".bedpe"),").")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"cnv")),(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"string")),(0,r.kt)("td",{parentName:"tr",align:null},"Required. An URL of the CNV text file (",(0,r.kt)("inlineCode",{parentName:"td"},".tsv"),").")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"drivers")),(0,r.kt)("td",{parentName:"tr",align:null},(0,r.kt)("inlineCode",{parentName:"td"},"string")),(0,r.kt)("td",{parentName:"tr",align:null},"Optional. 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A textual annotation.")))),(0,r.kt)("p",null,"A single-sample example:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-js"},'{\n "id": "7a921087-8e62-4a93-a757-fd8cdbe1eb8f",\n "cancer": "ovarian",\n "assembly": "hg19",\n "sv": "https://s3.amazonaws.com/gosling-lang.org/data/SV/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.pcawg_consensus_1.6.161022.somatic.sv.bedpe",\n "cnv": "https://s3.amazonaws.com/gosling-lang.org/data/SV/7a921087-8e62-4a93-a757-fd8cdbe1eb8f.consensus.20170119.somatic.cna.annotated.txt"\n}\n')),(0,r.kt)("p",null,"A multi-sample example:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-js"},'[\n {\n "id": "SRR7890905",\n "cancer": "breast",\n "assembly": "hg38",\n "drivers": "https://gist.githubusercontent.com/sehilyi/350b9e633c52ad97df00a0fc13a8839a/raw/c47b9ba33f1c9e187c69d1dadd01838db44d3b29/driver.txt",\n "sv": "https://somatic-browser-test.s3.amazonaws.com/SVTYPE_SV_test_tumor_normal_with_panel.bedpe",\n "cnv": "https://gist.githubusercontent.com/sehilyi/6fbceae35756b13472332d6b81b10803/raw/596428a8b0ebc00e7f8cbc52b050db0fbd6e19a5/SRR7890943.ascat.v3.cnv.tsv",\n "bam": "https://somatic-browser-test.s3.amazonaws.com/SRR7890905_GAPFI2USVS21.bam",\n "bai": "https://somatic-browser-test.s3.amazonaws.com/SRR7890905_GAPFI2USVS21.bam.bai",\n "note": "This is a test note"\n },\n {\n "id": "bc0dee07-de20-44d6-be65-05af7e63ac96",\n "cancer": "gastric",\n "assembly": "hg19",\n "sv": "https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/bc0dee07-de20-44d6-be65-05af7e63ac96.pcawg_consensus_1.6.161116.somatic.sv.bedpe",\n "cnv": "https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/bc0dee07-de20-44d6-be65-05af7e63ac96.consensus.20170119.somatic.cna.txt",\n "vcf": "https://somatic-browser-test.s3.amazonaws.com/cdk12cancers/bc0dee07-de20-44d6-be65-05af7e63ac96.consensus.20160830.somatic.snv_mnv.sorted.vcf.gz",\n "vcfIndex": 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