Simon Murray's repositories
clustering_investigation
Multiple scripts that visualize clustering data, generate heatmaps, produce statistics of Seurat data and compare clustering of different algorithms.
contribution-guide
A guide to repositories I have contributed to in my career.
systems_biology_coursework
GitHub repo for completing systems biology coursework module
testing_episcanpy
Script running RNA seq steps: normalization, calculating variability, clustering and visualisation with a new package called episcanpy.
DNA-pipeline
Nextflow DNA Seq Pipeline that performs: Quality Control, Alignment, Removing Duplicates, Variant Calling and Variant Annotation
testing_sphinx
Scripts that initialize and execute the sphinx software which has been integrated with graphviz to produce custom graphs for website publication.
bioconvert
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
cellbender_scripts
Scripts that run cellbender remove-background which removes technical artifacts and submit it for execution on compute nodes on a cluster.
conda-package-publish-action
Automatically Publishes Conda Packages To Anaconda
COVID-19
Forked repository of Covid19 Outbreak Data
configs
Config files used to define parameters specific to compute environments at different Institutions
covid-19-outbreak-tool
Script that automatically downloads latest covid19 data, produces plots tracking latest developments before uploading latest data and graphs to a website.
Covid19_outbreak
Website produced by covid-19-outbreak-tool hosting graphs tracking covid19 cases, deaths and recoveries. The data can be downloaded from the website.
database_coursework
Script that produces database using sqlite3 and populates it with covid19 testing data.
dbgap_data_extraction
Scripts used to fetch and extra data from the dbgap database before analyzing the data with star fusion and star rem.
docker-playground
A place for playing with Dockerfile
dotplot_fasta
A program that produces a dotplot diagram that can compare short DNA, RNA and protein sequences as described below.
machine_learning_coursework
Script that curates and explores expression data. This data is then used to train and test machine learning algorithms that then predict cancer in a new dataset. Logistic regression, tree modeling and neural networks were used.
omero_validation
Python script that validates input files ready for OMERO stitching and upload
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
scanpy_soupx
Repo which takes output from starsolo analysis and analyses it with scanpy and soupx
sceasy
A package to help convert different single-cell data formats to each other
SimonDMurray
Repository for containing my GitHub profile welcome page
statistics_introduction
Script that performs multiple statistical tests on multiple sets of input data and generates statistical plots.
synteny
An nf-core compliant Nextflow pipeline for running synteny analysis.
test-github-actions
Created and tested GitHub actions used to build, test and publish packages to Anaconda and PyPI for the repo hemberg-lab/sc3s.
test-tower-CI
Testing using GitHub Actions in conjunction with Nextflow Tower
University-Major-Project
Evidence of all scripts used in University Major Project for evidencing in University report
updating_adata_colourscheme
Script alters anndata objects to change colour scheme for plotting with cellxgene