Repositories list

• SAGC_WB_magpie

  Public
  Code for 2024-5 internship program

  0•1•0•0•Updated Feb 20, 2025Feb 20, 2025

• mgikit

  Public
  mgikit is a collection of tools used to demultiplex fastq files and generate demultiplexing and quality reports.

  fastqdemultiplexingmgi

  Rust

  •

  Other

  •1•11•3•0•Updated Feb 20, 2025Feb 20, 2025

• filesender-mp

  Public
  Adapting filesender for SAGC use, adding functionalities

  Jupyter Notebook

  •1•1•1•0•Updated Jan 21, 2025Jan 21, 2025

• demultiplex

  Public
  Demultiplexing pipeline for sequencing data

  Nextflow

  •

  MIT License

  •42•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• test-datasets

  Public
  Test data to be used for automated testing with the nf-core pipelines

  MIT License

  •367•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• MultiQC

  Public
  Aggregate results from bioinformatics analyses across many samples into a single report.

  JavaScript

  •

  GNU General Public License v3.0

  •612•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• abacbs2024_workshop

  Public
  SAGC STOmics workshop for ABACBS2024

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• workshop_nfRNAseq

  Public
  https://sagc-bioinformatics.github.io/workshop_nfRNAseq/

  HTML

  •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

• nextflow-example-workflow-2024

  Public
  A complete example workflow for the 2024 nextflow-vs-snakemake workshop (https://github.com/sagc-bioinformatics/nextflow-vs-snakemake-2024)

  Nextflow

  •1•2•0•0•Updated Sep 17, 2024Sep 17, 2024

• nextflow-vs-snakemake-2024

  Public
  A homepage for our 2024 bioinformatics workflow managers workshop.

  HTML

  •2•2•0•0•Updated Aug 27, 2024Aug 27, 2024

• nectar-workshop-deployment

  Public
  Nectar setup for 2024 nextflow vs snakemake workshop

  Shell

  •0•0•0•0•Updated Aug 20, 2024Aug 20, 2024

• adapter-checks

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Aug 12, 2024Aug 12, 2024

• spatial-workshop-may9

  Public
  0•1•0•0•Updated May 8, 2024May 8, 2024

• streamlit-barcode-checker

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •2•0•2•0•Updated Feb 27, 2024Feb 27, 2024

• mgikit-multiqc

  Public
  MultiQC plugin to parse and integrate reports generated by mgikit demultiplexer

  Python

  •

  MIT License

  •0•0•1•0•Updated Jan 5, 2024Jan 5, 2024

• SAGC_scRNAseq_workshop

  Public
  SAGC scRNAseq workshop

  Python

  •2•0•0•0•Updated Nov 7, 2023Nov 7, 2023

• sagc-bioinformatics.github.io

  Public
  South Australian Genomics Centre

  HTML

  •0•0•0•0•Updated Aug 25, 2023Aug 25, 2023

• 2022-snakemake-workshop

  Public
  Snakemake workshop materials for the SAGC metagenomics + Snakemake workshop

  TeX

  •1•0•0•0•Updated Jul 5, 2022Jul 5, 2022

• workshop-sysadmin

  Public
  Shell

  •1•0•0•0•Updated Jul 4, 2022Jul 4, 2022

• configs

  Public
  Config files used to define parameters specific to compute environments at different Institutions

  Nextflow

  •

  MIT License

  •288•0•0•0•Updated Mar 17, 2022Mar 17, 2022

• snakemake_profiles

  Public
  Shell

  •0•0•0•0•Updated Dec 1, 2021Dec 1, 2021

• monolithic_bash_script_to_snakemake

  Public
  Shell

  •

  MIT License

  •2•1•0•0•Updated Nov 28, 2021Nov 28, 2021

• modules

  Public
  Module files for Nextflow workflows

  Nextflow

  •

  MIT License

  •4•2•1•0•Updated Nov 25, 2021Nov 25, 2021

• SAGC_5mCMethylation_tutorial

  Public
  WGBS tutorial

  HTML

  •

  MIT License

  •4•2•0•1•Updated Sep 21, 2021Sep 21, 2021

• snakemake_basic_template

  Public template
  A basic Snakemake template repo

  Python

  •0•0•1•0•Updated Aug 18, 2021Aug 18, 2021

• nf-BCR-ABL1-breakpoint

  Public
  Workflow version of Chung's previous pipeline which uses samtools and factera (v1.4.4)

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Aug 5, 2021Aug 5, 2021

• Bulk_RNAseq

  Public
  Bulk RNA-seq & Differential Gene Expression Analysis Workshop Material

  R

  •5•1•0•0•Updated Jul 7, 2021Jul 7, 2021

• nf-rnaseq-sagc

  Public
  RNAseq quantification pipeline

  Nextflow

  •2•1•0•0•Updated May 6, 2021May 6, 2021

• workshop-agrigenomics

  Public
  Shell

  •

  Creative Commons Attribution Share Alike 4.0 International

  •0•0•0•0•Updated Apr 13, 2021Apr 13, 2021