Repositories list

• EDAinR

  Public
  0•0•3•0•Updated Jan 23, 2025Jan 23, 2025

• Bioinformatics

  Public
  A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

  bioinformaticssnpsgenomics+ 16nextflowcancersomatic-variantsngsmetagenomicsbioinformatics-pipelinernaseq+ 9

  1•15•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

  pythonnotebookwasm+ 2pyodidemarimo

  Python

  •

  Apache License 2.0

  •9•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• ONT-bacpac-nf

  Public
  Bacterial profiling workflow for ONT data, written in Nextflow.

  Nextflow

  •

  GNU General Public License v3.0

  •0•1•12•0•Updated Jan 13, 2025Jan 13, 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

• proteinfold

  Public
  Protein 3D structure prediction pipeline

  Nextflow

  •

  MIT License

  •45•0•0•0•Updated Dec 13, 2024Dec 13, 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

• usyd-gadi-onboarding-guide

  Public
  User guide for onboarding USyd users to NCI Gadi

  CSS

  •

  MIT License

  •0•0•0•0•Updated Nov 28, 2024Nov 28, 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 Nov 19, 2024Nov 19, 2024

• clause-segmenter

  Public
  A clause segmenting tool utilising Python's SpaCy

  pythonnlpspacy

  Python

  •

  MIT License

  •0•0•1•0•Updated Nov 19, 2024Nov 19, 2024

• xskill-nim

  Public
  Notebook and data for NVIDIA-NIM cross skilling session

  Jupyter Notebook

  •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

• fea-workshop-2024

  Public
  R

  •0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

• observable-crate

  Public
  Experimenting with using Observable Framework on an RO-Crate

  TypeScript

  •0•0•19•0•Updated Nov 5, 2024Nov 5, 2024

• cellbender-contained

  Public
  Ubuntu 16.04 and Cuda 10.2 for https://cellbender.readthedocs.io/en/latest/

  Dockerfile

  •3•0•0•0•Updated Nov 4, 2024Nov 4, 2024

• stats-resources

  Public
  SIH Statistics resources

  HTML

  •

  Other

  •3•7•0•0•Updated Oct 28, 2024Oct 28, 2024

• .github

  Public
  0•0•0•1•Updated Oct 24, 2024Oct 24, 2024

• hello-nextflow

  Public
  Training materials for a Nextflow beginners workshop 2024

  Shell

  •3•3•0•0•Updated Oct 24, 2024Oct 24, 2024

• Germline-StructuralV-nf

  Public
  Germline structural variant calling pipeline for short read WGS datasets

  workflownextflowmanta+ 13bamsurvivorstructural-variantssmoovetidditgermline-variant-callingannotsv+ 6

  Nextflow

  •

  GNU General Public License v3.0

  •5•5•6•0•Updated Oct 23, 2024Oct 23, 2024

• 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

• 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