Sydney Informatics Hub (@Sydney-Informatics-Hub)
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Sydney-Informatics-Hub

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Top repositories

1

Shotgun-Metagenomics-Analysis

Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
Shell
17
star
2

Fastq-to-BAM

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi
Shell
14
star
3

Bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
9
star
4

dataharvester

Preprocess, aggregate, visualise and download geospatial data from a range of Australian (and international) data sources
R
9
star
5

stats-resources

SIH Statistics resources
HTML
7
star
6

usydColours

University of Sydney colour palettes for ggplot2
R
6
star
7

copy_xlsx_styles

Tool to copy excel styles from an exemplar to a dumped data worksheet
Python
6
star
8

AgReFed-ML

Machine learning tools for modelling and predicting agriculture systems and their uncertainties.
Jupyter Notebook
5
star
9

Somatic-ShortV

Shell
5
star
10

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
5
star
11

wahis-scraper

Scraper for disease outbreak reports on WAHIS, the OIE World Organisation for Animal Health data portal
Python
4
star
12

Germline-StructuralV-nf

Germline structural variant calling pipeline for short read WGS datasets
Nextflow
4
star
13

geodata-harvester

Jumpstart your geospatial analysis with a ready-made set of spatial-temporal aligned raster maps and data frames
Jupyter Notebook
4
star
14

labarchives-stoichiometry-widget

Stoichiometry Table widget for LabArchives ELN
JavaScript
4
star
15

aigis

Tools for aerial and satellite imagery acquisition, processing, annotation, and analysis using artificial intelligence
Python
4
star
16

recocam

Extract and process image annotations stored in EXIF data, and prepare camera trap data for camtrapr
R
4
star
17

eeharvest

Convenient methods for downloading Google Earth Engine images in Python
Python
3
star
18

xnat-uploader

Command-line tool for batch uploading of DICOMs to XNAT
Python
3
star
19

Scalable-DIA-NN

Scalable workflow to run https://github.com/vdemichev/DiaNN on NCI Gadi HPC
Shell
3
star
20

training.artemis.introhpc

Repo for Intro to HPC course
CSS
2
star
21

geopython

Introduction to Python for Geoscientists
Jupyter Notebook
2
star
22

AgReFed-Workshop

Workshop documentation, workflows and use-case examples for AgReFed DataHarvester and GEE in Python and R.
Jupyter Notebook
2
star
23

nf-core-demo

Demo nf workflow for unlocking nf-core workshop
Groovy
2
star
24

ChatGPT-Masterclass

Slides for the ChatGPT Masterclass
2
star
25

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.
Shell
2
star
26

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
Perl
2
star
27

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
2
star
28

geopython-pawsey

Introduction to Machine Learning with Python for Mineral Exploration. Rendered at https://sydney-informatics-hub.github.io/geopython-pawsey
Jupyter Notebook
2
star
29

training.artemis.python

Parallel computing with Python for HPC https://sydney-informatics-hub.github.io/training.artemis.python/
Python
2
star
30

PIPE-4002-EarthByte-ModelAtlas

SIH repo for work on PIPE-4002
Jupyter Notebook
1
star
31

Gadi-benchmarking

Template scripts to automate submission of identical benchmark tasks with increasing compute resources
Shell
1
star
32

training-RNAseq

RNA-seq data analysis course on Artemis HPC
HTML
1
star
33

training.artemis

Overview page for Artemis Training series
Python
1
star
34

tidbits

SIH's "tech tidbits" blog for sharing useful tools and tips
HTML
1
star
35

carbon-volcanics

With Ben Mather
Jupyter Notebook
1
star
36

training.blockchain

Blockchain for research
HTML
1
star
37

masterclass-distributional-regression

Slides for the May 2023 Masterclass on Distributional Regression
TeX
1
star
38

Slivar_VCFfiltering

Running Slivar CLI tool to query and filter group/trio VCF files
Shell
1
star
39

tiff2vrml

Takes a stack of TIFF files and converts to a 3D VRML file
Jupyter Notebook
1
star
40

Germline-ShortV

Shell
1
star
41

atap_corpus

Corpus is an extendable lite framework that provides a standardised base corpus structure for the collection of ATAP tools.
Python
1
star
42

qualtrics-pandas

Qualtrics export to pandas.DataFrame
Python
1
star
43

HASS-29_Quotation_Tool

Text analytics tool to extract quotes in a text.
Python
1
star
44

PIPE-3431-HiC-Data-Analysis

Scripts for running CHiCAGO for Capture HiC data analysis
Python
1
star
45

Module3R

Learn Machine Learning in the browser or locally in your RStudio IDE with interactive tutorials
1
star
46

aerial-annotation

Open source annotations tools for aerial imagery. Part of https://github.com/Sydney-Informatics-Hub/PIPE-3956-aerial-segmentation
Jupyter Notebook
1
star
47

RNAseq-DE-nf

Nextflow implementation of the RNAseq-DE workflow configured for NCI Gadi
Nextflow
1
star
48

llm-experiments

Experiments and prototypes working with large language models and their applications.
Python
1
star
49

Iak3dSIH

Increment-averaged kriging for 3D prediction of soil properties
R
1
star
50

PIPE-3956-aerial-segmentation

Open source aerial segmentation models.
1
star
51

Gen3-data-dictionary-dev

Python
1
star
52

nswcaselaw

Python module for searching and downloading judgments from NSW CaseLaw
Python
1
star
53

split-GeneWiz-fastq

Split GeneWiz 'combined' (concatenated) fastq files into correct flowcell-lane pairs
Perl
1
star
54

LLM-LCT-sequencing

AI Semantic Insights: LLM Toolkit for Analysing Educational Practices and Knowledge Building.
Python
1
star