Repositories list

• egg5_dias_CEN_config

  Public
  MIT License

  •0•2•1•0•Updated Feb 7, 2025Feb 7, 2025

• ici_reports_export

  Public
  This is a script to query ICIs API and get any

  MIT License

  •0•0•0•1•Updated Feb 7, 2025Feb 7, 2025

• automated-archiving

  Public
  Python script to monitor archiving on DNANexus

  pythondnanexus

  Python

  •0•2•4•0•Updated Feb 7, 2025Feb 7, 2025

• eggd_plot_variant_baf

  Public
  Plots BAF and depth of variants from given VCF

  R

  •

  MIT License

  •0•0•4•0•Updated Feb 7, 2025Feb 7, 2025

• NGS_Tar_deletion

  Public
  automated deletion of NGS .tar files on DNAnexus

  0•0•0•1•Updated Feb 7, 2025Feb 7, 2025

• egg4_dias_TWE_config

  Public
  Config for the Dias TWE assay

  0•1•0•0•Updated Feb 7, 2025Feb 7, 2025

• egg1_dias_TSO_config

  Public
  Config for the Dias TSO assay

  Python

  •0•2•0•0•Updated Feb 7, 2025Feb 7, 2025

• eggd_001_Reference

  Public
  Perl

  •1•1•9•2•Updated Feb 7, 2025Feb 7, 2025

• eggd_fusioninspector

  Public
  solidcancer

  Shell

  •

  MIT License

  •0•2•0•1•Updated Feb 6, 2025Feb 6, 2025

• themis

  Public
  Code for internal bioinformatics team auditing

  Python

  •

  MIT License

  •0•3•2•1•Updated Feb 6, 2025Feb 6, 2025

• uranus_nf_core_mini

  Public
  A mini uranus mostly nf-core pipeline that incorporates mosdepth, cggpindel (not nf-core) and sentieon bwamem

  Nextflow

  •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• eggd_conductor_configs

  Public
  Repository of eggd_conductor app and assay config files

  0•0•2•0•Updated Feb 6, 2025Feb 6, 2025

• eggd_picardqc

  Public
  Shell

  •0•0•6•0•Updated Feb 5, 2025Feb 5, 2025

• sd_wgs_monitoring

  Public
  Solid cancer WGS repository to monitor new files and new outputs from WGS workbooks jobs

  MIT License

  •0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

• MegaQC

  Public
  Web application to collect and visualise data across multiple MultiQC runs.

  Python

  •

  GNU General Public License v3.0

  •27•1•0•0•Updated Feb 5, 2025Feb 5, 2025

• eggd_vep_CENCNV_config

  Public
  Json configuration file for CEN CNV annotation using VEP.

  MIT License

  •0•0•1•0•Updated Feb 3, 2025Feb 3, 2025

• exon_file_and_g2t_from_new_refseq_gff

  Public
  Scripts to convert refseq gff to tsv and convert that tsv into a g2t file

  Python

  •0•2•0•0•Updated Feb 3, 2025Feb 3, 2025

• dx_job_monitor

  Public
  Check if the 002 jobs completed correctly and sends notifications

  Python

  •0•1•0•0•Updated Feb 2, 2025Feb 2, 2025

• eggd_multiqc

  Public
  Shell

  •0•1•0•1•Updated Feb 1, 2025Feb 1, 2025

• eggd_generate_variant_workbook

  Public
  DNAnexus app for generating xlsx variant workbooks

  Python

  •0•3•12•0•Updated Jan 30, 2025Jan 30, 2025

• eggd_dias_reports_workflow

  Public
  Workflow definition for Dias reports

  0•1•1•0•Updated Jan 30, 2025Jan 30, 2025

• eggd_vep_CEN_config

  Public
  Json configuration file for the implementation of VEP for the CEN assay.

  MIT License

  •0•1•1•0•Updated Jan 29, 2025Jan 29, 2025

• eggd_vep

  Public
  Shell

  •0•1•9•0•Updated Jan 29, 2025Jan 29, 2025

• eggd_vep_TWE_config

  Public
  Json configuration file for the implementation of VEP for the TWE assay.

  MIT License

  •0•1•1•0•Updated Jan 29, 2025Jan 29, 2025

• eggd_vep_uranus_config

  Public
  Json configuration file for the implementation of VEP for the MYE assay.

  0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

• eggd_TSO500_reports_workflow

  Public
  Shell

  •0•1•0•0•Updated Jan 28, 2025Jan 28, 2025

• athena

  Public
  Provides HTML reports with detailed coverage analysis for clinical NGS data.

  coveragengspython+ 1bioinformatics

  HTML

  •

  MIT License

  •2•4•13•0•Updated Jan 28, 2025Jan 28, 2025

• code_school

  Public
  HTML

  •1•3•0•2•Updated Jan 26, 2025Jan 26, 2025

• eggd_vcf_handler_for_uranus

  Public
  Python

  •0•1•1•0•Updated Jan 25, 2025Jan 25, 2025

• eggd_vep_helios_config

  Public
  MIT License

  •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025