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@bartongroup Geoff Barton's Computational Biology Group

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    71 repositories

    • LBS-comparison

      Public
      This is a GitHub Repository containing the data and code used for a thorough comparison of 11 ligand binding site prediction tools
      Jupyter Notebook
      •1•6•0•0•Updated Oct 14, 2024Oct 14, 2024

    • PT_interogate_m6anet_results

      Public
      Determine exon location of predicted m6a methylation sites
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • dexdash

      Public
      Interactive explorer for differential expression analysis centred on the volcano plot. Features fast functional enrichment.
      R
      •
      Other
      •0•2•0•0•Updated Oct 4, 2024Oct 4, 2024

    • PT_identify_polyA_sites

      Public
      script to identify polyA start sites in nanopore direct RNAseq data mapped to a genome
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

    • DDUpred

      Public
      Random forest based predictor for DDU compounds
      R
      •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

    • slivka

      Public
      Python
      •
      Apache License 2.0
      •3•7•28•1•Updated Aug 30, 2024Aug 30, 2024

    • slivka-bio

      Public
      Bioinformatics command line tools wrapped as slivka services with customisations for access from Jalview
      Python
      •
      Apache License 2.0
      •1•2•4•0•Updated Aug 19, 2024Aug 19, 2024

    • dexdata

      Public
      Example data for dexdash package
      R
      •
      Other
      •0•0•0•0•Updated Aug 16, 2024Aug 16, 2024

    • PT_Arabidopsis_names_to_annot

      Public
      annotates At names.
      0•0•0•0•Updated Aug 15, 2024Aug 15, 2024

    • FRAGSYS

      Public
      Jupyter Notebook
      •
      MIT License
      •0•5•0•0•Updated Aug 12, 2024Aug 12, 2024

    • MG_T6SS_tn-seq

      Public
      Analysis of Ssp4 and Ssp6 effects on Pseudomonas fluorescens using Tn-seq (Coulthurst)
      R
      •0•0•0•0•Updated Aug 7, 2024Aug 7, 2024

    • MG_ChromCom2

      Public
      Chromatin compaction 2 (Tanaka)
      R
      •0•0•0•0•Updated Aug 1, 2024Aug 1, 2024

    • ProIntVar

      Public
      The core bits of ProIntVar
      Python
      •
      MIT License
      •0•2•8•0•Updated Jul 29, 2024Jul 29, 2024

    • SM_VarAlign

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 29, 2024Jul 29, 2024

    • Colabfold_batch_installer

      Public
      Automated colabfold installation for UoD HPC Cluster
      Shell
      •0•1•0•0•Updated Jul 25, 2024Jul 25, 2024

    • MG_NCCProt

      Public
      Nascent Chromatin Capture Proteomics (Alabert)
      R
      •0•0•0•0•Updated Jun 25, 2024Jun 25, 2024

    • MG_COVIDProt_neutrophils

      Public
      Large-scale proteomics of COVID neutrophils (Chalmers)
      R
      •0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • fenr

      Public
      Fast functional enrichment.
      R
      •
      Other
      •0•0•0•0•Updated Jun 14, 2024Jun 14, 2024

    • PT_HiFi_rhizobial_assemblies

      Public
      scripts to assemble PacBio HiFi data from rhizobial microbiome
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jun 7, 2024Jun 7, 2024

    • covid19-ace2-variants

      Public
      Research code and data to interpret the effect of ACE2 variants on SARS-CoV-2 infection
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated May 2, 2024May 2, 2024

    • RNAit

      Public
      Reimplementation of RNAit RNAi primer selection tool
      HTML
      •
      MIT License
      •2•0•0•0•Updated Apr 24, 2024Apr 24, 2024

    • ProteoFAV

      Public
      Open-source framework for simple and fast integration of protein structure data with sequence annotations and genetic variation
      pythonbioinformaticsstructural-biologypdbannotationspandasvariantsdata-analysisfeaturesmmcif
      Python
      •
      MIT License
      •0•3•13•0•Updated Mar 1, 2024Mar 1, 2024

    • SM_Pfam-gnomAD-statistics

      Public
      Repository containing notebooks to compute statistics in the paper "A unified approach to evolutionary conservation and population constraint in proteins".
      MIT License
      •0•1•0•0•Updated Mar 1, 2024Mar 1, 2024

    • slivka-bio-docker

      Public
      Docker Compose configuration for slivka-bio
      Dockerfile
      •
      Apache License 2.0
      •1•1•0•1•Updated Feb 20, 2024Feb 20, 2024

    • fenr-shiny-example

      Public
      Example of a Shiny app for fast enrichment package fenr
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 18, 2024Jan 18, 2024

    • DRSASP-NoD-Docker

      Public
      Docker configuration for NoD
      Dockerfile
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 18, 2024Jan 18, 2024

    • MG_sulfRNAseq

      Public
      Re-analysis of public data to compare to COVID RNA-seq results (Chalmers)
      R
      •0•0•0•0•Updated Jan 17, 2024Jan 17, 2024

    • MG_UbiMito

      Public
      Mitochondrial ubiquitin landscape in neurons
      R
      •1•0•0•0•Updated Jan 15, 2024Jan 15, 2024

    • MG_PlantInfection

      Public
      How are Phytophthora effectors taken into plant cells? (Birch)
      R
      •0•0•0•0•Updated Jan 15, 2024Jan 15, 2024

    • statistics_course

      Public
      Figures for lectures on statistics
      R
      •0•1•0•0•Updated Nov 20, 2023Nov 20, 2023