Sydney-Informatics-Hub | GitHub owners

Sydney-Informatics-Hub/all-the-folds-and-some

Testing various protein modelling tools

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Sydney-Informatics-Hub/juxtorpus

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Sydney-Informatics-Hub/nswcaselaw

Python module for searching and downloading judgments from NSW CaseLaw

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Sydney-Informatics-Hub/stats-resources

SIH Statistics resources

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Sydney-Informatics-Hub/training-calendar-scraper

Scrape the SIH training calendar and generate HTML for use in the newsletter

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Sydney-Informatics-Hub/training_dresa

This repository will host the csv files for DReSA export

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Sydney-Informatics-Hub/sih-github-dashboard

A dashboard displaying contributions to repositories within the SIH organisation

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Sydney-Informatics-Hub/Module3R

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

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Sydney-Informatics-Hub/hansard-rights-data-vis

Data visualisation of UK Hansard data using Observable Framework

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Sydney-Informatics-Hub/tidbits

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

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Sydney-Informatics-Hub/ONT-bacpac-nf

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Sydney-Informatics-Hub/Nextflow_DSL2_template Fork of AustralianBioCommons/Nextflow_DSL2_template

Template for creating Nextflow DSL2 pipelines

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Sydney-Informatics-Hub/usydColours

University of Sydney colour palettes for ggplot2

Language: R - Size: 1010 KB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 6 - Forks: 2

Sydney-Informatics-Hub/Parabricks-Genomics-nf

Scalable Nextflow implementation of Parabricks genomics workflow.

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Sydney-Informatics-Hub/Bio-toolkit

Utility scripts and templates for public bioinformatics work

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Sydney-Informatics-Hub/ables Fork of AustralianBioCommons/ables

Australian BioCommons Leadership Share (ABLeS) documentation

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Sydney-Informatics-Hub/ldac-profile Fork of Language-Research-Technology/ldac-profile

LDAC specific RO Crate Profile

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Sydney-Informatics-Hub/Gen3-data-dictionary-dev

Language: Python - Size: 161 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

Sydney-Informatics-Hub/EDAinR

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Sydney-Informatics-Hub/knowledgebase

Content for linking to USYD knowledgebase

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Sydney-Informatics-Hub/AgReFed-ML

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

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Sydney-Informatics-Hub/eeharvest

Convenient methods for downloading Google Earth Engine images in Python

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Sydney-Informatics-Hub/xnat-uploader

Command-line tool for batch uploading of DICOMs to XNAT

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Sydney-Informatics-Hub/SIH_Masterclass

Size: 5.66 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/Scalable-DIA-NN

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

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Sydney-Informatics-Hub/xeus-python-demo

Demo of Jupyterlite with custom packages

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Sydney-Informatics-Hub/nirvana-contained

Language: Dockerfile - Size: 2.93 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/myrepo_masterclass

masterclass repo

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Sydney-Informatics-Hub/lessons_mlr_tidymodels

Lesson material for the SIH Machine Learning with R and tidymodels course

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Sydney-Informatics-Hub/PIPE-3955-NimbusBioImageTesting

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Sydney-Informatics-Hub/oni-loader

testbed for downloading corpora from LDaCA/ATAP

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Sydney-Informatics-Hub/wordcloud_matrix

Display subcorpora as a matrix of word clouds

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Sydney-Informatics-Hub/wahis-scraper

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

Language: Python - Size: 5.86 KB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 4 - Forks: 1

Sydney-Informatics-Hub/training.home

Home of SIH training courses

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Sydney-Informatics-Hub/training.smm Fork of Sydney-Informatics-Hub/training.alphafold

Image Segmentation Workflows for Sydney Microscopy and Microanalysis

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Sydney-Informatics-Hub/workshopbmc

Repository for WORKSHOP landing page for 2018 BMC partner course

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Sydney-Informatics-Hub/training.blockchain

Blockchain for research

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Sydney-Informatics-Hub/singularity

How to setup Singularity on your local machine

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Sydney-Informatics-Hub/training-template-old

Template for training websites

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Sydney-Informatics-Hub/training-template

SIH Quatro training template for R and Python

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Sydney-Informatics-Hub/tiff2vrml

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

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Sydney-Informatics-Hub/training.artemis.interhpc

Repo for Intermediate HPC course

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Sydney-Informatics-Hub/training.alphafold

AlphaFold predictions of protein structure on Sydney Research Compute Infrastructure

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Sydney-Informatics-Hub/SomaticShortV_makePON-nf

Make the Panel of Normals to be used for the Somatic short variant pipeline

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Sydney-Informatics-Hub/training.artemis.interhpc_broken

Intermediate HPC course

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Sydney-Informatics-Hub/training.artemis

Overview page for Artemis Training series

Language: Python - Size: 2.9 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

Sydney-Informatics-Hub/Somatic-shortV-nf

A nextflow workflow for calling Somatic short Variant using gatk

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Sydney-Informatics-Hub/scArches-contained Fork of Sydney-Informatics-Hub/megadetector-contained

Docker and Singularity workflow for running the scArches

Language: Python - Size: 18.6 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1

Sydney-Informatics-Hub/Slivar_VCFfiltering

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

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Sydney-Informatics-Hub/training-RNAseq-slides

Slides for the RNA-seq training course

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Sydney-Informatics-Hub/template-nf

A straightforward Nextflow workflow template generator.

Size: 374 KB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/SIH-Raijin-Trinity

Fast, scalable RNA-Seq de novo assembly with Trinity

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Sydney-Informatics-Hub/SIH-Artemis-Trinity

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Sydney-Informatics-Hub/rstan-contained

A container to run RStan on a Centos 6.10 host.

Language: Dockerfile - Size: 7.81 KB - Last synced: about 2 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/SIH-HPC-WGS

Pipeline for high throughput, scalable and efficient analysis of mammalian whole genome sequence

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Sydney-Informatics-Hub/RStudio_github_versioncontrol

masterclass which discusses how using RStudio for version control of R Markdown based projects with github

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Sydney-Informatics-Hub/SIH-DUG-Trinity

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Sydney-Informatics-Hub/rnaseq-workshop-2023

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Sydney-Informatics-Hub/split-GeneWiz-fastq

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

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Sydney-Informatics-Hub/OmixLitMiner Fork of vijayr1912/proteomicsliteratureminer

A bioinformatics tool for prioritising biological leads from omics data using literature mining.

Language: R - Size: 6.6 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 4

Sydney-Informatics-Hub/SIH-Flashlite-Trinity

Language: Shell - Size: 8.79 KB - Last synced: about 2 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/ro-crate-validate

Simple utility for validating RO-Crates

Language: Python - Size: 45.9 KB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 1

Sydney-Informatics-Hub/OHDSI-synpuf-postgres

Loads the SYNPUF 1000 person dataset into a docker postgres container

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Sydney-Informatics-Hub/QC-tools

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Sydney-Informatics-Hub/rna-differential-expression-Rnotebook

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

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Sydney-Informatics-Hub/qualtrics-pandas

Qualtrics export to pandas.DataFrame

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Sydney-Informatics-Hub/proquest-xml

Python module for parsing ProQuest XML files

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Sydney-Informatics-Hub/oni-ui Fork of Language-Research-Technology/oni-ui

LDaCA discovery portal for Heurist

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Sydney-Informatics-Hub/PIPE-3034-obesity2

Australian Obesity Corpus analysis

Language: R - Size: 30.9 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/padlet-scraper

Tools for scraping data (including reactions, comments) out of Padlet

Language: Python - Size: 2.93 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/OHDSI-Broadsea Fork of OHDSI/Broadsea

Broadsea deploys the full OHDSI technology stack (R methods library & web tools), using cross-platform Docker container technology.

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Sydney-Informatics-Hub/obesity_ukAus

Australian vs UK corpus comparison

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Sydney-Informatics-Hub/monai

Workflow to run MonAI label from Slicer3D on a Ronin virtual machine

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Sydney-Informatics-Hub/micro-sam-contained

Contaier for micro-sam https://github.com/computational-cell-analytics/micro-sam

Language: Dockerfile - Size: 5.86 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/obesitycorpus

Professor Monika Bednarek obesity project - source code

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Sydney-Informatics-Hub/nf-coreConfigs

Language: Shell - Size: 23.4 KB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 1

Sydney-Informatics-Hub/intro-git

An introduction to Git

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Sydney-Informatics-Hub/Nextflow_DSL2_template_guide

Self-directed materials for using the Nextflow DSL2 template

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Sydney-Informatics-Hub/myrepo_masterclass_RStudio

Creating a repo for masterclass

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Sydney-Informatics-Hub/IGVreport-nf

Generate html variant summary report with IGV

Language: Nextflow - Size: 26.4 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/mlpy-binder

Language: Jupyter Notebook - Size: 417 KB - Last synced: about 2 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/hydromad Fork of josephguillaume/hydromad

Hydrological Model Assessment and Development

Language: R - Size: 6.62 MB - Last synced: about 2 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/jenkins_docker_test

Language: Python - Size: 7.18 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/Iak3dSIH

Increment-averaged kriging for 3D prediction of soil properties

Language: R - Size: 191 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

Sydney-Informatics-Hub/model-validation

This repository provides a template workflow and stating point for evaluating the performance of deployed models for achieving their target task.

Language: Jupyter Notebook - Size: 11.7 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/matlab-contained

Matlab in a docker container for centos 6.9

Language: Dockerfile - Size: 7.81 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/llm-experiments

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

Language: Python - Size: 229 KB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

Sydney-Informatics-Hub/lessonbmc

BMC Lesson materials

Language: HTML - Size: 14.3 MB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 2

Sydney-Informatics-Hub/lesson-shiny

Materials for our shiny training

Language: R - Size: 5.31 MB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 1

Sydney-Informatics-Hub/LLM-finetuning-seminar

LLM fine-tuning tutorial and example notebook for OpenAI GPT finetuning

Language: Jupyter Notebook - Size: 6.38 MB - Last synced: about 2 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

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

Language: Perl - Size: 27.3 KB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 2 - Forks: 0

Sydney-Informatics-Hub/heurist-to-rocrate

Language: PHP - Size: 68.4 KB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/GPUnoCUDA

Language: C - Size: 167 KB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/HASS-29_Quotation_Tool

Text analytics tool to extract quotes in a text.

Language: Python - Size: 12 MB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

Sydney-Informatics-Hub/gorilla-cli-testing

Size: 1.95 KB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/gis2coco Fork of hlydecker/gis2coco

Convert geospatial datasets of shapefiles and rasters into COCO format datasets of images and JSON.

Language: Python - Size: 35.2 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

GitHub / Sydney-Informatics-Hub 189 repositories