Repositories list

• EJohnson_calcium_collagen_trimerisation

  Public
  R

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  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated Jan 28, 2026Jan 28, 2026

• SkeletalVis-Transcriptomics

  Public
  Nextflow pipeline for microarray and RNA-seq

  rna-seqnextflowmicroarray+ 2transcriptomicspathway-analysis

  R

  •0•1•2•0•Updated Dec 5, 2025Dec 5, 2025

• Leptospira-LIC13259-C8G

  Public
  Code to reproduce work in paper titled 'AlphaFold reveals how pathogenic Leptospira use thiol-disulphide exchange to evade the complement membrane attack comple…

  structural-biologystructural-bioinformatics

  Shell

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  MIT License

  •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• animal_ageing

  Public
  KS4 activity to introduce students to plotting with Python.

  pythonoutreachteaching-materials+ 1outreach-activities

  Jupyter Notebook

  •0•0•2•0•Updated Jul 20, 2025Jul 20, 2025

• AdenomyosisGeoMX

  Public
  Spatial transcriptomics analysis of adenomyosis lesions

  R

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  MIT License

  •0•0•0•0•Updated Jun 12, 2025Jun 12, 2025

• MicroAge_Proteomics_paper

  Public
  R

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  MIT License

  •0•0•0•0•Updated Apr 15, 2025Apr 15, 2025

• SingleCellCourseWebsite

  Public
  Website for the Single Cell Course

  github-pagescoursesingle-cell-rna-seq+ 1quarto

  CSS

  •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

• jSLE_paper

  Public
  0•0•0•0•Updated Mar 25, 2025Mar 25, 2025

• RIF_Spatial

  Public
  GeoMX spatial transcriptomics analysis of endometrial tissue from individuals with recurrent implantation failure or fertile controls

  R

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  MIT License

  •0•1•0•0•Updated Feb 21, 2025Feb 21, 2025

• SCPSampleAnnotationWizard

  Public
  Generates sample annotation .csv files to be passed to the colData argument in the readSCP() function from the scp R package.

  JavaScript

  •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

• Gene_expression_dysregulation_in_whole_blood_of_patients_with_C_difficile_infection

  Public
  R

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  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated Nov 28, 2024Nov 28, 2024

• quarto-omics-template

  Public
  quarto template for starting omics analysis

  R

  •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

• PubLLican_curated_data_assembly

  Public
  Assembling and formating for all curated GO term data from VEuPathDB

  R

  •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

• Astuti_et_al_2023

  Public
  R code to accompany the publication

  R

  •0•1•0•0•Updated Nov 14, 2024Nov 14, 2024

• ML_Kidney_Tx

  Public
  Python

  •0•1•0•0•Updated Oct 15, 2024Oct 15, 2024

• Sulfo_Tyrosine

  Public
  Searching for Sulfotyrosines (sY) in a HA(pY)STACK

  proteomicsmass-spectrometryphosphorylation+ 3meta-analysistyrosine-sulfationptm-misidentification

  Python

  •0•1•0•0•Updated Oct 9, 2024Oct 9, 2024

• RICE_AF2

  Public
  Python

  •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

• Epigenetics-OA-Risk-Human-Skeletal-Dev

  Public
  Methylation and mqtl analysis of the developing knee

  methylationcolocalizationmqtl+ 2genotypingosteoarthritis

  R

  •0•0•0•0•Updated Aug 7, 2024Aug 7, 2024

• preprocessing_plasma_SPRINT

  Public
  R

  •0•0•0•0•Updated May 13, 2024May 13, 2024

• neonatalIntestinal_fecalBacteriaInflammation

  Public
  R

  •0•0•0•0•Updated May 2, 2024May 2, 2024

• InflammatorySkinGeoMX

  Public
  Spatial transcriptomics analysis of inflammatory skin diseases

  skinpsoriasisspatial-transcriptomics+ 1geomx

  R

  •0•1•0•0•Updated Jan 17, 2024Jan 17, 2024

• EffectorScan-prototype

  Public
  Identification of novel effectors among unique fungal genes (fusarium oxysporum).

  R

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  Apache License 2.0

  •0•1•0•0•Updated Jan 5, 2024Jan 5, 2024

• SERPINA3Chondrogenesis

  Public
  R

  •0•0•0•0•Updated Nov 13, 2023Nov 13, 2023

• IntroductionToTidyModels

  Public
  Introduction to machine learning with tidymodels

  machine-learningtidymodelsepigenetic-clock

  HTML

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  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 19, 2023Jun 19, 2023

• northernbug.github.io

  Public
  The NorthernBUG Website

  HTML

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  MIT License

  •3.8k•0•0•0•Updated Jun 19, 2023Jun 19, 2023

• Raymant-et-al-2023

  Public
  single-cell-rna-seq

  HTML

  •0•0•0•0•Updated May 20, 2023May 20, 2023

• Turlo_MSC_secretome_proteomics

  Public
  time-seriesimputationproteomics+ 1nmf

  HTML

  •0•0•0•0•Updated Feb 3, 2023Feb 3, 2023

• SkeletalVis-ATACSeq

  Public
  Nextflow pipeline for analysis of ATAC-sequencing data

  nextflowatac-seq

  R

  •0•0•0•0•Updated Nov 18, 2022Nov 18, 2022

• googlemaps_simple_demo

  Public
  Very simple google maps demo

  JavaScript

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  MIT License

  •0•0•0•0•Updated Aug 18, 2022Aug 18, 2022

• mapping_and_enrichment

  Public
  Collection of code that maps IDs and does enrichment.

  functional-enrichment-analysisnon-model-species

  R

  •0•0•1•0•Updated Jun 21, 2022Jun 21, 2022