https://github.com/sydney-informatics-hub/shotgun-metagenomics-analysis

Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more

Last synced: 18 Jul 2025

https://github.com/sydney-informatics-hub/bioinformatics

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

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts cancer genomics germline-variants indels metagenomics nextflow nextflow-pipelines ngs research-computing rnaseq snps somatic-variants sydney-informatics-hub transcriptomics variant-calling

Last synced: 11 Feb 2026

https://github.com/sydney-informatics-hub/fastq-to-bam

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

bioinformatics bwa-mem gatk-bestpractices mapping ngs sequencing

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/dataharvester

Preprocess, aggregate, visualise and download geospatial data from a range of Australian (and international) data sources

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/usydcolours

University of Sydney colour palettes for ggplot2

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/stats-resources

SIH Statistics resources

Last synced: 07 Oct 2025

https://github.com/sydney-informatics-hub/copy_xlsx_styles

Tool to copy excel styles from an exemplar to a dumped data worksheet

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/somatic-shortv

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/germline-structuralv-nf

Germline structural variant calling pipeline for short read WGS datasets

annotsv australian-biocommons bam bioinformatics dsl2 genomics germline-variant-calling manta nextflow ngs pipeline smoove structural-variants survivor tiddit workflow

Last synced: 02 Jan 2026

https://github.com/sydney-informatics-hub/geodata-harvester

Jumpstart your geospatial analysis with a ready-made set of spatial-temporal aligned raster maps and data frames

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/recocam

Extract and process image annotations stored in EXIF data, and prepare camera trap data for camtrapr

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/aigis

Tools for aerial and satellite imagery acquisition, processing, annotation, and analysis using artificial intelligence

aerial-imagery computer-vision geospatial gis python pytorch segmentation transformers

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/agrefed-ml

Machine learning tools for modelling and predicting agriculture systems and their uncertainties.

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/labarchives-stoichiometry-widget

Stoichiometry Table widget for LabArchives ELN

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/aerial-segmentation

Open source aerial imagery segmentation model fine tuning, evaluation, and prediction tools. Part of https://github.com/Sydney-Informatics-Hub/PIPE-3956-aerial-segmentation

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/wahis-scraper

Scraper for disease outbreak reports on WAHIS, the OIE World Organisation for Animal Health data portal

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/bootstrapping-for-bqsr

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.

Last synced: 25 Jul 2025

https://github.com/sydney-informatics-hub/eeharvest

Convenient methods for downloading Google Earth Engine images in Python

Last synced: 24 Jul 2025

https://github.com/sydney-informatics-hub/rnaseq-de

Last synced: 20 Feb 2026

https://github.com/sydney-informatics-hub/hello-nextflow

Training materials for a Nextflow beginners workshop 2024

Last synced: 18 Jul 2025

https://github.com/sydney-informatics-hub/template-nf

A straightforward Nextflow workflow template generator.

bioinformatics dsl2 genomics nextflow nextflow-pipeline pipeline template workflow

Last synced: 09 Feb 2026

https://github.com/sydney-informatics-hub/parabricks-genomics-nf

Scalable Nextflow implementation of germline alignment and short variant calling with Parabricks for NCI Gadi HPC.

Last synced: 27 Feb 2026

https://github.com/sydney-informatics-hub/scalable-dia-nn

Scalable workflow to run https://github.com/vdemichev/DiaNN on NCI Gadi HPC

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/xnat-uploader

Command-line tool for batch uploading of DICOMs to XNAT

Last synced: 18 Feb 2026

https://github.com/sydney-informatics-hub/agrefed-workshop

Workshop documentation, workflows and use-case examples for AgReFed DataHarvester and GEE in Python and R.

Last synced: 22 Aug 2025

https://github.com/sydney-informatics-hub/geopython-pawsey

Introduction to Machine Learning with Python for Mineral Exploration. Rendered at https://sydney-informatics-hub.github.io/geopython-pawsey

Last synced: 03 Feb 2026

https://github.com/sydney-informatics-hub/germline-shortv

Last synced: 10 Mar 2026

https://github.com/sydney-informatics-hub/training-rnaseq

RNA-seq data analysis course on Artemis HPC

Last synced: 03 Jan 2026

https://github.com/sydney-informatics-hub/training.artemis.python

Parallel computing with Python for HPC https://sydney-informatics-hub.github.io/training.artemis.python/

Last synced: 24 Jan 2026

https://github.com/sydney-informatics-hub/aerial-annotation

Open source annotations tools for aerial imagery. Part of https://github.com/Sydney-Informatics-Hub/PIPE-3956-aerial-segmentation

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/ont-bacpac-nf

Bacterial profiling workflow for ONT data, written in Nextflow.

Last synced: 12 Feb 2026

https://github.com/sydney-informatics-hub/hpc_usage_reports

Scripts to pull resource usage data from job logs for Artemis and Gadi into tab-delimited format and to report queue time from job history

artemis gadi hpc nci-gadi nextflow nf-core usyd-artemis

Last synced: 04 Jul 2025

https://github.com/sydney-informatics-hub/rocrate-abstract

ROCrate Python library aimed at crates over the network

Last synced: 01 Feb 2026

https://github.com/sydney-informatics-hub/chatgpt-masterclass

Slides for the ChatGPT Masterclass

Last synced: 19 Mar 2026

https://github.com/sydney-informatics-hub/module3r

Learn Machine Learning in the browser or locally in your RStudio IDE with interactive tutorials

Last synced: 05 Jan 2026

https://github.com/sydney-informatics-hub/training.artemis.introhpc

Repo for Intro to HPC course

Last synced: 14 Jun 2025

https://github.com/sydney-informatics-hub/nf-core-demo

Demo nf workflow for unlocking nf-core workshop

Last synced: 05 Jul 2025

https://github.com/sydney-informatics-hub/aerial-conversion

Open source tools enabling interchange between computer vision annotation and GIS data formats. Part of https://github.com/Sydney-Informatics-Hub/PIPE-3956-aerial-segmentation

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/geopython

Introduction to Python for Geoscientists

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/hass-29_quotation_tool

Text analytics tool to extract quotes in a text.

Last synced: 28 Jul 2025

https://github.com/sydney-informatics-hub/gadi-benchmarking

Template scripts to automate submission of identical benchmark tasks with increasing compute resources

Last synced: 20 Jul 2025

https://github.com/sydney-informatics-hub/langchainlaw

Langchain for classifying judgments

Last synced: 06 Mar 2026

https://github.com/sydney-informatics-hub/nswcaselaw

Python module for searching and downloading judgments from NSW CaseLaw

Last synced: 12 Jun 2025

https://github.com/sydney-informatics-hub/rna-differential-expression-rnotebook

An R notebook for RNaseq differential expression and functional enrichment analysis.

Last synced: 19 Mar 2026

https://github.com/sydney-informatics-hub/llm-lct-sequencing

AI Semantic Insights: LLM Toolkit for Analysing Educational Practices and Knowledge Building.

classification knowledge-representation llm

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/usyd-gadi-onboarding-guide

User guide for onboarding USyd users to NCI Gadi

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/training.artemis

Overview page for Artemis Training series

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/gen3-data-dictionary-dev

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/rocrate-tabular

Python library for converting an RO-Crate to tabular representations

Last synced: 25 Jun 2025

https://github.com/sydney-informatics-hub/masterclass-distributional-regression

Slides for the May 2023 Masterclass on Distributional Regression

Last synced: 19 Mar 2026

https://github.com/sydney-informatics-hub/tidbits

SIH's "tech tidbits" blog for sharing useful tools and tips

Last synced: 19 Mar 2026

https://github.com/sydney-informatics-hub/bio-toolkit

Resource library and utility scripts and templates for public bioinformatics work

Last synced: 02 Jan 2026

https://github.com/sydney-informatics-hub/slivar_vcffiltering

Running Slivar CLI tool to query and filter group/trio VCF files

Last synced: 14 Oct 2025

https://github.com/sydney-informatics-hub/tower-nf

Notes, helper scripts, instructions for running nextflow tower

Last synced: 28 Oct 2025

https://github.com/sydney-informatics-hub/pipe-4002-earthbyte-modelatlas

SIH repo for work on PIPE-4002

Last synced: 06 Jan 2026

https://github.com/sydney-informatics-hub/marsupial

Lightning fast animal detection and identification models.

Last synced: 12 Jul 2025

https://github.com/sydney-informatics-hub/iak3dsih

Increment-averaged kriging for 3D prediction of soil properties

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/training.blockchain

Blockchain for research

Last synced: 03 Jan 2026

https://github.com/sydney-informatics-hub/carbon-volcanics

With Ben Mather

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/germlineshortv_biovalidation

Workflow for biological validation of germline SNP and indel variant datasets.

germline indel snp validation variant-analysis variant-calling wgs wholegenomesequencing

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/sih-raijin-trinity

Fast, scalable RNA-Seq de novo assembly with Trinity

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/pipe-3431-hic-data-analysis

Scripts for running CHiCAGO for Capture HiC data analysis

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/tiff2vrml

Takes a stack of TIFF files and converts to a 3D VRML file

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/split-genewiz-fastq

Split GeneWiz 'combined' (concatenated) fastq files into correct flowcell-lane pairs

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/llm-experiments

Experiments and prototypes working with large language models and their applications.

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/qualtrics-pandas

Qualtrics export to pandas.DataFrame

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/template-nf-guide

Self-directed materials for using the Nextflow DSL2 template

Last synced: 30 Jul 2025

https://github.com/sydney-informatics-hub/xskill-nim

Notebook and data for NVIDIA-NIM cross skilling session

Last synced: 30 Jul 2025

https://github.com/sydney-informatics-hub/ace3tool

ACE-III online dementia screening tool

Last synced: 08 Sep 2025

https://github.com/sydney-informatics-hub/tabpfn_seminar

AI-Powered Tabular Modeling with TabPFN

Last synced: 04 Mar 2025

https://github.com/sydney-informatics-hub/bioinformatics_licenses

Links and other details for licensed softwares at SIH

Last synced: 07 Feb 2026

https://github.com/sydney-informatics-hub/microscopy-segmentation

Electron Microscopy Segmentation - SMM Colab Pilot Study

Last synced: 26 Jul 2025

https://github.com/sydney-informatics-hub/glottolog-lookup

Python script to find Glottolog ids for language names

Last synced: 13 Oct 2025

https://github.com/sydney-informatics-hub/biocommons-canu-metrics

Collect compute usage metrics from NCI Gadi BioCommons Canu Workflow

Last synced: 20 Jul 2025

https://github.com/sydney-informatics-hub/obesity_ukaus

Australian vs UK corpus comparison

Last synced: 10 Jul 2025

https://github.com/sydney-informatics-hub/igvreport-nf

Generate html variant summary report with IGV

Last synced: 03 Jan 2026

https://github.com/sydney-informatics-hub/spaceranger-contained

stereopy and spaceranger for docker/singularity centos7

Last synced: 30 Jan 2026

https://github.com/sydney-informatics-hub/somatic-shortv-nf

A nextflow workflow for calling Somatic short Variant using gatk

Last synced: 03 Jan 2026

https://github.com/sydney-informatics-hub/nf-coreconfigs

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/xskill-gitpod

Two demo scenarios for gitpod: training and collaborative code dev. Used juxtorpus and hello-nextflow.

Last synced: 03 Jan 2026

https://github.com/sydney-informatics-hub/ohdsi-synpuf-postgres

Loads the SYNPUF 1000 person dataset into a docker postgres container

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/sih-github-dashboard

A dashboard displaying contributions to repositories within the SIH organisation

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/sih_masterclass

Last synced: 03 Jan 2026

https://github.com/sydney-informatics-hub/myrepo_masterclass_rstudio

Creating a repo for masterclass

Last synced: 03 Jan 2026

https://github.com/sydney-informatics-hub/mlpy-binder

Last synced: 30 Oct 2025

https://github.com/sydney-informatics-hub/pipe-3519-machine-learning-in-veterinary-medicine

Last synced: 04 Feb 2026

https://github.com/sydney-informatics-hub/myrepo_masterclass

masterclass repo

Last synced: 03 Jan 2026

https://github.com/sydney-informatics-hub/flashlite-supernova

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/gorilla-cli-testing

Last synced: 03 Jan 2026

https://github.com/sydney-informatics-hub/bio-test-datasets

Subset bioinformatics datasets for workflow development and testing

Last synced: 05 Feb 2026

https://github.com/sydney-informatics-hub/observable-crate

Experimenting with using Observable Framework on an RO-Crate

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/somaticshortv-nf

A DSL2-nextflow pipeline for GATK based Somatic Short-Variant identification

Last synced: 03 Jan 2026

https://github.com/sydney-informatics-hub/spacy-explain

This is an explainer notebook for SpaCy Part-of-Speech, Part-of-Speech (fine-grained), and Dependency tags

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/deepflash2-contained

Deepflash container

Last synced: 02 Jan 2026

https://github.com/sydney-informatics-hub/tower-hpc-user-guide

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/training.artemis.interhpc_broken

Intermediate HPC course

Last synced: 03 Jan 2026

https://github.com/sydney-informatics-hub/lessonbmc

BMC Lesson materials

Last synced: 17 Feb 2026

https://github.com/sydney-informatics-hub/training.home

Home of SIH training courses

Last synced: 23 Jul 2025

https://github.com/sydney-informatics-hub/training-template

SIH Quatro training template for R and Python

Last synced: 15 Mar 2025

https://github.com/sydney-informatics-hub/lessons-mlpy-part2

Machine learning in Python part 1: classification models

Last synced: 15 Mar 2025