Repositories list

• PCPBFull

  Public
  A software pipeline to reproduce results in the paper 'Flawed machine-learning confounds coding sequence annotation' by the Gardner Lab

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 27, 2025May 27, 2025

• PCPBSlim

  Public
  Data and results for the paper "Flawed machine-learning confounds coding sequence annotation"

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 27, 2025May 27, 2025

• TISIGNER-ReactJS

  Public
  TISIGNER: Unleash the power of synthetic biology

  structural-biologywebserversynthetic-biology+ 8

  structural-biologywebserversynthetic-biologymultiprocessingproteinsolubilityrna-structuresimulated-annealingtranslation-initiation-sitebiotechnology+ 1

  JavaScript

  •

  Other

  •66 forks•3030 stars•00 issues•1212 pull requests•Updated May 24, 2025May 24, 2025

• Razor_paper_2021

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 31, 2025Jan 31, 2025

• Enterobacteriaceae-TraDIS

  Public
  Gnuplot

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 15, 2025Jan 15, 2025

• TIsigner_paper_2019

  Public
  Code related to TIsigner manuscript and webserver

  bioinformaticsstructural-biologymultiprocessing+ 5

  bioinformaticsstructural-biologymultiprocessingproteinrna-structuresimulated-annealingtranslation-initiation-sitebiotechnology

  Jupyter Notebook

  •

  Other

  •00 forks•22 stars•00 issues•00 pull requests•Updated Nov 16, 2024Nov 16, 2024

• Avoidance-v2

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•11 pull request•Updated Jun 17, 2024Jun 17, 2024

• invasive_salmonella

  Public
  Data and code to accompany our paper on identifying patterns of gene degradation associated with invasiveness in Salmonella

  Perl

  •

  GNU General Public License v3.0

  •11 fork•99 stars•11 issue•00 pull requests•Updated Apr 26, 2023Apr 26, 2023

• PPI_Analysis_2022

  Public
  An accurate, scalable and generalisable tool for predicting protein-protein interactions

  Python

  •00 forks•22 stars•11 issue•00 pull requests•Updated Nov 4, 2022Nov 4, 2022

• TIsigner

  Public
  Translation Initiation coding region designer

  bioinformaticsstructural-biologywebserver+ 6

  bioinformaticsstructural-biologywebservermultiprocessingproteinrna-structuresimulated-annealingtranslation-initiation-sitebiotechnology

  CSS

  •

  Other

  •33 forks•33 stars•00 issues•33 pull requests•Updated Jun 21, 2022Jun 21, 2022

• speed-vs-accuracy-meta-analysis

  Public
  scripts and datasets associated with a study of benchmarks of bioinformatic software

  TeX

  •

  Other

  •33 forks•33 stars•00 issues•00 pull requests•Updated Jan 21, 2022Jan 21, 2022

• genome-randomisation-survey

  Public
  A survey of methods for randomising genome sequences

  Perl

  •

  Creative Commons Zero v1.0 Universal

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 22, 2021Dec 22, 2021

• thesis-bikash

  Public
  Final version uwu 😊

  latex

  latex

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 2, 2021Nov 2, 2021

• Streptococcus-pyogenes

  Public
  Streptococcus pyogenes

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 20, 2021Aug 20, 2021

• deltaBS

  Public
  Quantifying the significance of genetic variation using probabilistic profile-based methods.

  TeX

  •

  MIT License

  •11 fork•1919 stars•11 issue•00 pull requests•Updated Apr 21, 2021Apr 21, 2021

• Razor

  Public
  Tool to predict eukaryotic signal peptides. In addition, prediction of toxin and fungi signal peptides is also done.

  fungicleavage-sitessignal-peptide+ 1

  fungicleavage-sitessignal-peptidetoxic-proteins

  Python

  •

  Other

  •11 fork•66 stars•11 issue•00 pull requests•Updated Feb 22, 2021Feb 22, 2021

• SoDoPE_paper_2020

  Public
  Jupyter Notebook

  •55 forks•1111 stars•00 issues•00 pull requests•Updated Jan 2, 2021Jan 2, 2021

• ncVarDB

  Public
  Repo for the ncVAR database

  R

  •44 forks•55 stars•11 issue•00 pull requests•Updated Oct 13, 2020Oct 13, 2020

• Non-codingDBS

  Public
  A repository to keep files for Delta-bitscore non-coding variation project.

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 15, 2020Jun 15, 2020

• Compartmentalisation_Marsden2019

  Public
  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 3, 2020Apr 3, 2020

• EnTrI

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 13, 2020Mar 13, 2020

• beth-thesis

  Public
  Gnuplot

  •11 fork•00 stars•00 issues•11 pull request•Updated Feb 27, 2020Feb 27, 2020

• uniqueome2

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Nov 27, 2019Nov 27, 2019

• robustness-RNP

  Public
  A series of comparisons of the mutational robustness of RNAs and proteins.

  HTML

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 14, 2019Nov 14, 2019

• twilight_zone

  Public
  Manuscript, code, important data

  Perl

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 8, 2019May 8, 2019

• RNA_Interactions_Benchmark

  Public
  RNA-RNA interaction predictions tools benchmark scripts, wrappers and datafiles.

  Python

  •

  MIT License

  •11 fork•88 stars•11 issue•00 pull requests•Updated Feb 28, 2019Feb 28, 2019

• invasive_campylobacter

  Public
  Data and code to accompany our work on invasive Campylobacter isolates

  Perl

  •00 forks•22 stars•00 issues•00 pull requests•Updated Dec 11, 2018Dec 11, 2018

• meta-analysis-eDNA-software

  Public
  A meta-analysis of environmental DNA sequence analysis benchmarks

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 15, 2018Oct 15, 2018

• sRNA_evo

  Public
  Beths sRNA evolution project, and other scripts

  Perl

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 26, 2018Sep 26, 2018

• Avoidance

  Public
  RNA avoidance scripts and data.

  R

  •

  MIT License

  •22 forks•11 star•00 issues•00 pull requests•Updated Mar 7, 2018Mar 7, 2018