Geoff Barton's Computational Biology Group's repositories
LBS-comparison
This is a GitHub Repository containing the data and code used for a thorough comparison of 11 ligand binding site prediction tools
PT_identify_polyA_sites
script to identify polyA start sites in nanopore direct RNAseq data mapped to a genome
DDUpred
Random forest based predictor for DDU compounds
slivka-bio
Bioinformatics command line tools wrapped as slivka services with customisations for access from Jalview
dexdata
Example data for dexdash package
PT_Arabidopsis_names_to_annot
annotates At names.
MG_T6SS_tn-seq
Analysis of Ssp4 and Ssp6 effects on Pseudomonas fluorescens using Tn-seq (Coulthurst)
PT_interogate_m6anet_results
Determine exon location of predicted m6a methylation sites
MG_ChromCom2
Chromatin compaction 2 (Tanaka)
Colabfold_batch_installer
Automated colabfold installation for UoD HPC Cluster
MG_NCCProt
Nascent Chromatin Capture Proteomics (Alabert)
MG_COVIDProt_neutrophils
Large-scale proteomics of COVID neutrophils (Chalmers)
fenr
Fast functional enrichment.
PT_HiFi_rhizobial_assemblies
scripts to assemble PacBio HiFi data from rhizobial microbiome
covid19-ace2-variants
Research code and data to interpret the effect of ACE2 variants on SARS-CoV-2 infection
RNAit
Reimplementation of RNAit RNAi primer selection tool
SM_Pfam-gnomAD-statistics
Repository containing notebooks to compute statistics in the paper "A unified approach to evolutionary conservation and population constraint in proteins".
slivka-bio-docker
Docker Compose configuration for slivka-bio
fenr-shiny-example
Example of a Shiny app for fast enrichment package fenr
DRSASP-NoD-Docker
Docker configuration for NoD
MG_sulfRNAseq
Re-analysis of public data to compare to COVID RNA-seq results (Chalmers)
MG_UbiMito
Mitochondrial ubiquitin landscape in neurons
MG_PlantInfection
How are Phytophthora effectors taken into plant cells? (Birch)
statistics_course
Figures for lectures on statistics