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    237 repositories

    • xskill-gitpod

      Public
      Two demo scenarios for gitpod: training and collaborative code dev. Used juxtorpus and hello-nextflow.
      0•0•0•1•Updated Oct 21, 2024Oct 21, 2024

    • observable-crate

      Public
      Experimenting with using Observable Framework on an RO-Crate
      TypeScript
      •0•0•18•0•Updated Oct 18, 2024Oct 18, 2024

    • ONT-bacpac-nf

      Public
      Bacterial profiling workflow for ONT data, written in Nextflow.
      Nextflow
      •
      GNU General Public License v3.0
      •0•1•14•0•Updated Oct 18, 2024Oct 18, 2024

    • .github

      Public
      0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • stats-resources

      Public
      SIH Statistics resources
      HTML
      •
      Other
      •3•7•0•0•Updated Oct 15, 2024Oct 15, 2024

    • LLM-LCT-sequencing

      Public
      AI Semantic Insights: LLM Toolkit for Analysing Educational Practices and Knowledge Building.
      classificationknowledge-representationllm
      Python
      •
      MIT License
      •0•1•2•0•Updated Oct 15, 2024Oct 15, 2024

    • OmixLitMiner

      Public
      A bioinformatics tool for prioritising biological leads from omics data using literature mining.
      HTML
      •
      MIT License
      •5•3•3•0•Updated Oct 11, 2024Oct 11, 2024

    • ace3tool

      Public
      ACE-III online dementia screening tool
      TypeScript
      •1•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • rshinyapp-template

      Public
      R
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • hello-nextflow

      Public
      Training materials for a Nextflow beginners workshop 2024
      Shell
      •1•1•0•0•Updated Oct 9, 2024Oct 9, 2024

    • juxtorpus

      Public
      Jupyter Notebook
      •1•0•1•0•Updated Oct 7, 2024Oct 7, 2024

    • knowledgebase

      Public
      Content for linking to USYD knowledgebase
      0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • ro_crate_graph

      Public
      Tool for turning an RO-Crate into lists of nodes and links
      Python
      •0•0•0•0•Updated Sep 27, 2024Sep 27, 2024

    • Bioinformatics_licenses

      Public
      Links and other details for licensed softwares at SIH
      0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

    • tidbits

      Public
      SIH's "tech tidbits" blog for sharing useful tools and tips
      HTML
      •0•1•1•0•Updated Sep 25, 2024Sep 25, 2024

    • whisper-speaker-diarization

      Public
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Sep 24, 2024Sep 24, 2024

    • Fastq-to-VCF

      Public
      High throughput illumina mammalian whole genome sequence analysis and joint genotyping
      Shell
      •0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

    • template-nf-guide

      Public
      Self-directed materials for using the Nextflow DSL2 template
      CSS
      •
      MIT License
      •0•0•6•0•Updated Sep 18, 2024Sep 18, 2024

    • template-nf

      Public template
      A straightforward Nextflow workflow template generator.
      templateworkflowbioinformaticspipelinegenomicsnextflownextflow-pipelinedsl2
      0•2•6•0•Updated Sep 13, 2024Sep 13, 2024

    • marsupial

      Public
      Lightning fast animal detection and identification models.
      Jupyter Notebook
      •
      MIT License
      •3•2•0•0•Updated Sep 5, 2024Sep 5, 2024

    • hansard-normalised

      Public
      A project aimed at converting a collection of Hansard HTML snippets to a normalised dataset.
      Python
      •
      MIT License
      •0•0•4•0•Updated Sep 5, 2024Sep 5, 2024

    • bio-toolkit

      Public
      Resource library and utility scripts and templates for public bioinformatics work
      HTML
      •1•1•0•0•Updated Sep 5, 2024Sep 5, 2024

    • emailrag

      Public
      Local RAG with Ollama + Mac Mail mbox export
      Python
      •
      MIT License
      •205•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • training-calendar-scraper

      Public
      Scrape the SIH training calendar and generate HTML for use in the newsletter
      TypeScript
      •1•0•0•0•Updated Sep 1, 2024Sep 1, 2024

    • Parabricks-Genomics-nf

      Public
      Scalable Nextflow implementation of germline alignment and short variant calling with Parabricks for NCI Gadi HPC.
      Nextflow
      •
      GNU General Public License v3.0
      •1•2•2•0•Updated Aug 29, 2024Aug 29, 2024

    • LLM-local-RAG

      Public
      A locally-hosted Retrieval Augmented Generation pipeline for querying a Large Language Model on YOUR documents.
      Python
      •
      MIT License
      •2•0•0•0•Updated Aug 28, 2024Aug 28, 2024

    • SPUDNIG

      Public
      Linux version of SPUDNIG
      Python
      •3•0•0•0•Updated Aug 27, 2024Aug 27, 2024

    • Germline-StructuralV-nf

      Public
      Germline structural variant calling pipeline for short read WGS datasets
      workflownextflowmantabamsurvivorstructural-variantssmoovetidditgermline-variant-callingannotsv
      Nextflow
      •
      GNU General Public License v3.0
      •5•4•5•1•Updated Aug 27, 2024Aug 27, 2024

    • Bioinformatics

      Public
      A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.
      bioinformaticssnpsgenomicsnextflowcancersomatic-variantsngsmetagenomicsbioinformatics-pipelinernaseq
      1•12•0•0•Updated Aug 27, 2024Aug 27, 2024

    • Nextflow_DSL2_template

      Public
      Template for creating Nextflow DSL2 pipelines
      Nextflow
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Aug 25, 2024Aug 25, 2024