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    247 repositories

    • usyd-gadi-onboarding-guide

      Public
      User guide for onboarding USyd users to NCI Gadi
      CSS
      •
      MIT License
      •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

    • proteinfold

      Public
      Protein 3D structure prediction pipeline
      Nextflow
      •
      MIT License
      •49•0•0•0•Updated Feb 12, 2025Feb 12, 2025

    • rstan-contained

      Public
      A container to run RStan on a Centos 6.10 host.
      Dockerfile
      •0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

    • .github

      Public
      0•0•0•1•Updated Feb 12, 2025Feb 12, 2025

    • TabPFN_seminar

      Public
      AI-Powered Tabular Modeling with TabPFN
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

    • stats-resources

      Public
      SIH Statistics resources
      HTML
      •
      Other
      •3•7•0•0•Updated Feb 10, 2025Feb 10, 2025

    • EDAinR

      Public
      0•0•3•0•Updated Feb 6, 2025Feb 6, 2025

    • Module3R

      Public
      Learn Machine Learning in the browser or locally in your RStudio IDE with interactive tutorials
      R
      •
      MIT License
      •1•2•4•1•Updated Feb 4, 2025Feb 4, 2025

    • mercury

      Public
      Mercury concentration in fish with Prof. Elaine Baker and the Marine Studies Institute
      1•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • ONT-bacpac-nf

      Public
      Bacterial profiling workflow for ONT data, written in Nextflow.
      Nextflow
      •
      GNU General Public License v3.0
      •0•1•11•0•Updated Jan 31, 2025Jan 31, 2025

    • RNASeq-DE

      Public
      Shell
      •
      GNU General Public License v3.0
      •2•1•10•0•Updated Jan 28, 2025Jan 28, 2025

    • Somatic-ShortV

      Public
      Shell
      •
      GNU General Public License v3.0
      •2•8•11•0•Updated Jan 28, 2025Jan 28, 2025

    • Bootstrapping-for-BQSR

      Public
      Bootstrap a variant resource for non-model organisms that lack known variant databases. This is to enable GATK Base Quality Score Recalibration (BQSR) to be performed for improved variant calls.
      Shell
      •1•3•9•0•Updated Jan 28, 2025Jan 28, 2025

    • Germline-ShortV

      Public
      Shell
      •
      GNU General Public License v3.0
      •3•2•4•1•Updated Jan 28, 2025Jan 28, 2025

    • Fastq-to-BAM

      Public
      Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi
      mappingbwa-memgatk-bestpracticesbioinformaticsngssequencing
      Shell
      •
      GNU General Public License v3.0
      •7•20•7•0•Updated Jan 28, 2025Jan 28, 2025

    • Fastq-to-VCF

      Public
      High throughput illumina mammalian whole genome sequence analysis and joint genotyping
      Shell
      •0•0•1•0•Updated Jan 28, 2025Jan 28, 2025

    • Bioinformatics

      Public
      A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.
      bioinformaticssnpsgenomicsnextflowcancersomatic-variantsngsmetagenomicsbioinformatics-pipelinernaseq
      1•16•4•0•Updated Jan 21, 2025Jan 21, 2025

    • tidbits

      Public
      SIH's "tech tidbits" blog for sharing useful tools and tips
      HTML
      •0•1•1•0•Updated Jan 20, 2025Jan 20, 2025

    • training.artemis.introhpc

      Public template
      Repo for Intro to HPC course
      CSS
      •
      MIT License
      •2•2•2•0•Updated Jan 20, 2025Jan 20, 2025

    • training.artemis

      Public
      Overview page for Artemis Training series
      Python
      •
      Other
      •0•1•0•1•Updated Jan 20, 2025Jan 20, 2025

    • sih-marimo-gh-pages-template

      Public template
      A template repo for deploying marimo WebAssembly notebooks to GitHub Pages
      pythonnotebookwasmpyodidemarimo
      Python
      •
      Apache License 2.0
      •17•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • usydColours

      Public
      University of Sydney colour palettes for ggplot2
      R
      •2•9•1•0•Updated Jan 13, 2025Jan 13, 2025

    • ResearchPulseAI

      Public
      AI-driven Research Impact Assessment Tool and Case Study Generator for NSW Health
      0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • RefCheckAI

      Public
      AI Reference Checker: Automated citation validation for AI-generated and academic content.
      0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • juxtorpus

      Public
      Jupyter Notebook
      •1•0•1•0•Updated Dec 18, 2024Dec 18, 2024

    • hello-nextflow-amsi24

      Public
      Training materials for the AMSI BioInfoSummer24 Hello Nextflow workshop
      3•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • rocrate-abstract

      Public
      ROCrate Python library aimed at crates over the network
      Python
      •0•2•0•0•Updated Dec 9, 2024Dec 9, 2024

    • rocrate-tabular

      Public
      Python library for converting an RO-Crate to tabular representations
      Python
      •1•0•15•1•Updated Dec 9, 2024Dec 9, 2024

    • nextflow-demo

      Public
      Basic demo of real world Nextflow use
      Nextflow
      •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • Functional_Enrichment_BioCommons_2024

      Public
      Materials and resources for a 2-day workshop on functional enrichment analysis, organised by Australian BioCommons and delivered by Monash University and the University of Sydney.
      HTML
      •1•0•0•0•Updated Nov 29, 2024Nov 29, 2024