Repositories list

• workflows

  Public
  Bioinformatics workflows developed for and used on the St. Jude Cloud project.

  workflowbioinformaticsgenomics+ 8workflow-enginenext-generation-sequencingwdlcwlworkflowscromwellwdl-workflow+ 1

  WDL

  •

  MIT License

  •10•0•0•0•Updated Feb 1, 2021Feb 1, 2021

• mkdocs-ngenebio

  Public
  A Material Design theme for MkDocs

  materialmkdocsmkdocs-material

  TypeScript

  •

  MIT License

  •3.5k•0•0•0•Updated Feb 1, 2021Feb 1, 2021

• variantValidator

  Public
  Public repository for VariantValidator project

  validationnomenclaturevcf+ 1hgvs

  Python

  •

  GNU Affero General Public License v3.0

  •21•0•0•0•Updated Jan 28, 2021Jan 28, 2021

• pcgr

  Public
  Personal Cancer Genome Reporter (PCGR)

  genomicsciviccancer+ 4cgivepcosmictier

  R

  •

  MIT License

  •48•0•0•0•Updated Jan 25, 2021Jan 25, 2021

• react-mutation-plot

  Public
  A light weight adaptation React based mutation lollipop plot from cBioPortal frontend.

  JavaScript

  •

  GNU Affero General Public License v3.0

  •7•0•0•0•Updated Jan 21, 2021Jan 21, 2021

• rest_variantValidator

  Public
  REST Interface for VariantValidator. Includes docker container

  apirestvalidator+ 3vcfvarianthgvs

  Python

  •

  GNU Affero General Public License v3.0

  •47•0•0•0•Updated Jan 14, 2021Jan 14, 2021

• variantFormatter

  Public
  validationvarianthgvs

  Python

  •

  GNU Affero General Public License v3.0

  •4•0•0•0•Updated Jan 13, 2021Jan 13, 2021

• oliver

  Public
  An opinionated Cromwell orchestration manager.

  awsworkflowazure+ 2orchestrationcromwell

  Python

  •

  MIT License

  •3•0•0•0•Updated Jan 11, 2021Jan 11, 2021

• civicmine

  Public
  Text mining cancer biomarkers for the CIVIC database

  text-miningsnakemakecivic+ 3shinykindredbiotext

  R

  •

  MIT License

  •2•0•0•0•Updated Dec 3, 2020Dec 3, 2020

• sjcloud-data-transfer-app

  Public
  Application to securely upload data to and download data from St. Jude Cloud Platform.

  nodejsoauthgenomics+ 3downloaduploadeletron

  JavaScript

  •

  Apache License 2.0

  •2•0•0•0•Updated Nov 17, 2020Nov 17, 2020

• wdldoc

  Public
  Create WDL documentation using Markdown.

  markdowndocumentationwdl

  Python

  •

  MIT License

  •5•0•0•0•Updated Oct 29, 2020Oct 29, 2020

• vv_hgvs

  Public
  Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

  validationvariantshgvs

  Python

  •

  Apache License 2.0

  •94•0•0•0•Updated Oct 23, 2020Oct 23, 2020

• g3viz

  Public
  Lollipop-diagram to interactively visualize genetic mutations

  JavaScript

  •

  Other

  •19•0•0•0•Updated Aug 26, 2020Aug 26, 2020

• hgvs

  Public
  HGVS variant name parsing and generation

  pythonvarianthgvs

  Python

  •

  MIT License

  •79•0•0•0•Updated Apr 29, 2020Apr 29, 2020

• diagnostics_exome_reporting

  Public
  Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.

  Shell

  •

  GNU General Public License v3.0

  •10•0•0•0•Updated Nov 11, 2019Nov 11, 2019

• WES_ShinyDiscover

  Public
  A Shiny interface to filter and identify variants of interest from whole exome data

  CSS

  •

  GNU General Public License v3.0

  •5•0•0•0•Updated Sep 16, 2019Sep 16, 2019