Sydney Informatics Hub
The Sydney Informatics Hub is a Core Research Facility of the University of Sydney, providing training and expertise on research data, analysis and computing.
University of Sydney, Sydney Australia
Pinned Repositories
aigis
Tools for aerial and satellite imagery acquisition, processing, annotation, and analysis using artificial intelligence
Bioinformatics
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
copy_xlsx_styles
Tool to copy excel styles from an exemplar to a dumped data worksheet
dataharvester
Preprocess, aggregate, visualise and download geospatial data from a range of Australian (and international) data sources
Fastq-to-BAM
Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi
Shotgun-Metagenomics-Analysis
Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
Somatic-ShortV
stats-resources
SIH Statistics resources
tidbits
SIH's "tech tidbits" blog for sharing useful tools and tips
usydColours
University of Sydney colour palettes for ggplot2
Sydney Informatics Hub's Repositories
Sydney-Informatics-Hub/myrepo_masterclass_RStudio
Creating a repo for masterclass
Sydney-Informatics-Hub/myrepo_masterclass
masterclass repo
Sydney-Informatics-Hub/CQPweb-docker
SIH dockerized version of CQPweb
Sydney-Informatics-Hub/training.artemis
Overview page for Artemis Training series
Sydney-Informatics-Hub/selectio
Feature importance models and auto feature selection
Sydney-Informatics-Hub/cellranger-contained
Docker and Singularity workflow for running cellranger
Sydney-Informatics-Hub/scArches-contained
Docker and Singularity workflow for running the scArches
Sydney-Informatics-Hub/pytorch-contained
Docker and Singularity workflow for running pytorch
Sydney-Informatics-Hub/nfcoreWorkshopTesting
testing and materials development for AusBioCommons customising nf-core workshop 2023
Sydney-Informatics-Hub/dataharvester
Preprocess, aggregate, visualise and download geospatial data from a range of Australian (and international) data sources
Sydney-Informatics-Hub/Git_RStudio_masterclass
Getting started with Git in RStudio: a hands-on guide
Sydney-Informatics-Hub/lessons_mlr_tidymodels
Lesson material for the SIH Machine Learning with R and tidymodels course
Sydney-Informatics-Hub/monai
Workflow to run MonAI label from Slicer3D on a Ronin virtual machine
Sydney-Informatics-Hub/context-chatbot
Context-based chatbot using OpenAI ChatGPT.
Sydney-Informatics-Hub/twitter-ncapture
ncapture broke. This could be an alternative.
Sydney-Informatics-Hub/masterclass_RStudio_GitHub
for RStudio github masterclass
Sydney-Informatics-Hub/PIPE-3955-NimbusBioImageTesting
Sydney-Informatics-Hub/ChatGPT-Masterclass
Slides for the ChatGPT Masterclass
Sydney-Informatics-Hub/PIPE-3431-HiC-Data-Analysis
Scripts for running CHiCAGO for Capture HiC data analysis
Sydney-Informatics-Hub/autoTesting-nf
Automated testing testing for SIH Nextflow workflows
Sydney-Informatics-Hub/cvmfsTesting
Testing unpacked containers on CVMFS
Sydney-Informatics-Hub/chatGPT_masterclass
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.
Sydney-Informatics-Hub/AgReFed-Workshop
Workshop documentation, workflows and use-case examples for AgReFed DataHarvester and GEE in Python and R.
Sydney-Informatics-Hub/agrefed-server
Public server repo instructions for AgReFed
Sydney-Informatics-Hub/IGVreport-nf
Generate html variant summary report with IGV
Sydney-Informatics-Hub/gis2coco
Convert geospatial datasets of shapefiles and rasters into COCO format datasets of images and JSON.
Sydney-Informatics-Hub/bamQC-nf
Report summary statistics relating to quality of bam files with Nextflow
Sydney-Informatics-Hub/SomaticShortV_makePON-nf
Make the Panel of Normals to be used for the Somatic short variant pipeline
Sydney-Informatics-Hub/SomaticShortV-nf
A DSL2-nextflow pipeline for GATK based Somatic Short-Variant identification