Explore @Sydney-Informatics-Hub Open Source projects

Sydney Informatics Hub (@Sydney-Informatics-Hub)

Sydney-Informatics-Hub

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Location 🇦🇺 Australia
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Shotgun-Metagenomics-Analysis

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

Fastq-to-BAM

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

Bioinformatics

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

dataharvester

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

stats-resources

SIH Statistics resources

copy_xlsx_styles

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

AgReFed-ML

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

Jupyter Notebook

usydColours

University of Sydney colour palettes for ggplot2

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

Jupyter Notebook

Somatic-ShortV

aigis

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

Germline-StructuralV-nf

Germline structural variant calling pipeline for short read WGS datasets

wahis-scraper

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

geodata-harvester

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

Jupyter Notebook

labarchives-stoichiometry-widget

Stoichiometry Table widget for LabArchives ELN

recocam

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

eeharvest

Convenient methods for downloading Google Earth Engine images in Python

xnat-uploader

Command-line tool for batch uploading of DICOMs to XNAT

Scalable-DIA-NN

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

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

training.artemis.introhpc

Repo for Intro to HPC course

geopython

Introduction to Python for Geoscientists

Jupyter Notebook

AgReFed-Workshop

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

Jupyter Notebook

nf-core-demo

Demo nf workflow for unlocking nf-core workshop

ChatGPT-Masterclass

Slides for the ChatGPT Masterclass

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.

Module3R

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

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

Jupyter Notebook

geopython-pawsey

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

Jupyter Notebook

training.artemis.python

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

aerial-annotation

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

Jupyter Notebook

PIPE-4002-EarthByte-ModelAtlas

SIH repo for work on PIPE-4002

Jupyter Notebook

Gadi-benchmarking

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

training-RNAseq

RNA-seq data analysis course on Artemis HPC

training.artemis

Overview page for Artemis Training series

carbon-volcanics

With Ben Mather

Jupyter Notebook

training.blockchain

Blockchain for research

tidbits

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

Slivar_VCFfiltering

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

tiff2vrml

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

Jupyter Notebook

Germline-ShortV

atap_corpus

Corpus is an extendable lite framework that provides a standardised base corpus structure for the collection of ATAP tools.

qualtrics-pandas

Qualtrics export to pandas.DataFrame

masterclass-distributional-regression

Slides for the May 2023 Masterclass on Distributional Regression

PIPE-3431-HiC-Data-Analysis

Scripts for running CHiCAGO for Capture HiC data analysis

RNAseq-DE-nf

Nextflow implementation of the RNAseq-DE workflow configured for NCI Gadi

llm-experiments

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

HASS-29_Quotation_Tool

Text analytics tool to extract quotes in a text.

Iak3dSIH

Increment-averaged kriging for 3D prediction of soil properties

PIPE-3956-aerial-segmentation

Open source aerial segmentation models.

Gen3-data-dictionary-dev

nswcaselaw

Python module for searching and downloading judgments from NSW CaseLaw

split-GeneWiz-fastq

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

LLM-LCT-sequencing

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

rna-differential-expression-Rnotebook

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

marsupial

Lightning fast animal detection and identification models.

Jupyter Notebook

ONT-bacpac-nf

Bacterial profiling workflow for ONT data, written in Nextflow.

bio-toolkit

Resource library and utility scripts and templates for public bioinformatics work

tower-nf

Notes, helper scripts, instructions for running nextflow tower

langchainlaw

Langchain for classifying judgments