Discover Sydney-Informatics-Hub/Fastq-to-BAM Open Source project

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

Bioinformatics

dataharvester

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

stats-resources

SIH Statistics resources

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

copy_xlsx_styles

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

AgReFed-ML

University of Sydney colour palettes for ggplot2

usydColours

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

Somatic-ShortV

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

aigis

Germline structural variant calling pipeline for short read WGS datasets

Germline-StructuralV-nf

Nextflow

wahis-scraper

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

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

geodata-harvester

Stoichiometry Table widget for LabArchives ELN

labarchives-stoichiometry-widget

JavaScript

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

Command-line tool for batch uploading of DICOMs to XNAT

xnat-uploader

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

Scalable-DIA-NN

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

HPC_usage_reports

Perl

training.artemis.introhpc

Repo for Intro to HPC course

CSS

geopython

Introduction to Python for Geoscientists

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

AgReFed-Workshop

Demo nf workflow for unlocking nf-core workshop

nf-core-demo

Groovy

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.

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

Module3R

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

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

geopython-pawsey

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

training.artemis.python

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

aerial-annotation

SIH repo for work on PIPE-4002

PIPE-4002-EarthByte-ModelAtlas

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

Gadi-benchmarking

RNA-seq data analysis course on Artemis HPC

training-RNAseq

Overview page for Artemis Training series

training.artemis

carbon-volcanics

With Ben Mather

training.blockchain

Blockchain for research

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

tidbits

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

Slivar_VCFfiltering

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

tiff2vrml

Germline-ShortV

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

atap_corpus

Qualtrics export to pandas.DataFrame

qualtrics-pandas

Slides for the May 2023 Masterclass on Distributional Regression

masterclass-distributional-regression

TeX

PIPE-3431-HiC-Data-Analysis

Scripts for running CHiCAGO for Capture HiC data analysis

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

RNAseq-DE-nf

Nextflow

llm-experiments

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

Text analytics tool to extract quotes in a text.

HASS-29_Quotation_Tool

Increment-averaged kriging for 3D prediction of soil properties

Iak3dSIH

PIPE-3956-aerial-segmentation

Open source aerial segmentation models.

Gen3-data-dictionary-dev

Python module for searching and downloading judgments from NSW CaseLaw

nswcaselaw

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

split-GeneWiz-fastq

Perl

LLM-LCT-sequencing

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

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

rna-differential-expression-Rnotebook

Lightning fast animal detection and identification models.

marsupial

Bacterial profiling workflow for ONT data, written in Nextflow.

ONT-bacpac-nf

Nextflow

bio-toolkit

Resource library and utility scripts and templates for public bioinformatics work

Notes, helper scripts, instructions for running nextflow tower

tower-nf

Langchain for classifying judgments

langchainlaw