Repositories list

• GENEFLOW

  Public
  Genomic Examination and Nucleotide Evaluation For Laboratory Operations Workflow

  Python

  •1•0•4•2•Updated Jan 10, 2025Jan 10, 2025

• reform

  Public
  Modify existing reference fasta and gff3/gtf files to include a new sequence

  Python

  •6•30•1•1•Updated Jan 10, 2025Jan 10, 2025

• reformWeb

  Public
  Flask WebUI for reform

  Python

  •2•0•0•4•Updated Dec 2, 2024Dec 2, 2024

• hpc-gatk4

  Public
  Nextflow

  •0•0•1•0•Updated Jul 13, 2023Jul 13, 2023

• variant-calling-pipeline-gatk4

  Public
  Variant Calling Pipeline Using GATK4 and Nextflow

  bioinformaticsgenomicsnextflow+ 3bioinformatics-pipelinevariant-callinggatk4

  Nextflow

  •46•53•1•1•Updated Feb 16, 2023Feb 16, 2023

• MAD2

  Public
  Python

  •0•0•0•0•Updated Jul 27, 2022Jul 27, 2022

• django-shibboleth-remoteuser

  Public
  Middleware for using Shibboleth with Django

  Python

  •

  MIT License

  •75•0•0•0•Updated Jun 28, 2022Jun 28, 2022

• MAD

  Public
  Minor Allele Detection Pipeline for SARS-CoV2

  covid-19sars-cov-2sars-cov-2-variants+ 3bioinformaticsgenomicsngs

  Python

  •1•1•0•0•Updated Jul 15, 2021Jul 15, 2021

• covid19

  Public
  Variant Analysis Pipeline for COVID19

  Nextflow

  •1•4•0•0•Updated Apr 30, 2021Apr 30, 2021

• ReSeq

  Public
  More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original

  C++

  •

  MIT License

  •3•0•0•0•Updated Feb 13, 2021Feb 13, 2021

• mpileupplugin

  Public
  A JBrowse plugin for plotting allele fraction data

  JavaScript

  •1•0•0•0•Updated Jun 19, 2020Jun 19, 2020

• variant-calling-pipeline

  Public
  HPC based pipelines for variant calling using GATK

  Shell

  •23•17•0•0•Updated Apr 6, 2020Apr 6, 2020

• nf-workflows

  Public
  Repository of NextFlow Workflows

  Nextflow

  •0•4•0•0•Updated Mar 26, 2020Mar 26, 2020

• r-notebooks

  Public
  Gene Set Enrichment Analysis and Over Representation Analysis analysis using R

  bioinformaticsgenomicsgsea+ 2over-representation-analysisgene-set-enrichment-analysis

  25•19•3•0•Updated Jun 20, 2019Jun 20, 2019

• BADAS

  Public
  Collection of BADAS related resources

  Jupyter Notebook

  •0•1•0•0•Updated Oct 4, 2018Oct 4, 2018

• utils

  Public
  0•0•0•0•Updated Apr 27, 2018Apr 27, 2018