Repositories list

• website

  Public template
  PomBase website v2

  fission-yeastpombase

  TypeScript

  •

  MIT License

  •1•6•90•1•Updated Jan 16, 2025Jan 16, 2025

• pombase-legacy

  Public
  Code for handling legacy PomBase data

  Perl

  •

  MIT License

  •1•0•0•0•Updated Jan 16, 2025Jan 16, 2025

• pombase-chado

  Public
  PomBase code for accessing Chado

  Perl

  •

  MIT License

  •3•5•53•0•Updated Jan 16, 2025Jan 16, 2025

• pombase-config

  Public
  Shared configuration for PomBase projects

  Perl

  •2•0•4•0•Updated Jan 15, 2025Jan 15, 2025

• genome_changelog

  Public
  Python

  •

  MIT License

  •1•1•1•0•Updated Jan 15, 2025Jan 15, 2025

• allele_qc

  Public
  Quality control for PomBase alleles

  Python

  •

  MIT License

  •1•1•10•0•Updated Jan 15, 2025Jan 15, 2025

• fypo

  Public
  Fission Yeast Phenotype Ontology

  obofoundryphenotypesfission-yeast+ 1pombase

  Makefile

  •

  Creative Commons Attribution 4.0 International

  •6•15•112•1•Updated Jan 14, 2025Jan 14, 2025

• canto

  Public
  The PomBase community curation tool

  JavaScript

  •

  Other

  •7•19•182•1•Updated Jan 12, 2025Jan 12, 2025

• pombase-python-web

  Public
  Python web code for the PomBase project

  Python

  •1•0•0•0•Updated Jan 11, 2025Jan 11, 2025

• pombase-chado-json

  Public
  Read a PomBase Chado database and write it as JSON

  Rust

  •

  MIT License

  •1•1•0•0•Updated Jan 10, 2025Jan 10, 2025

• pombase-domain-process

  Public
  Extract the InterPro data for the PomBase proteins and write as JSON

  Rust

  •0•1•0•0•Updated Dec 2, 2024Dec 2, 2024

• curation

  Public
  PomBase curation

  biocurationfission-yeastpombase

  0•7•224•0•Updated Nov 17, 2024Nov 17, 2024

• mitochondrion

  Public
  0•0•14•0•Updated Oct 16, 2024Oct 16, 2024

• pombase-historic-go-stats

  Public
  PomBase historic GAF files

  Python

  •0•0•0•0•Updated Oct 12, 2024Oct 12, 2024

• chobo

  Public
  Code for loading OBO files into a Chado database using COPY (prototype)

  Perl

  •1•0•6•0•Updated Jun 6, 2024Jun 6, 2024

• canto_tutorial

  Public
  A static site with canto documentation for users to get started with Canto.

  Python

  •

  MIT License

  •0•2•0•0•Updated May 17, 2024May 17, 2024

• wc-gocam-viz

  Public
  Web component to visualize GO-CAMs

  TypeScript

  •

  BSD 3-Clause "New" or "Revised" License

  •2•0•0•0•Updated Nov 7, 2023Nov 7, 2023

• pombase-python

  Public
  PomBase Python code

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 1, 2023Nov 1, 2023

• all_previous_sgd_peptide_sequences

  Public
  A simple set of scripts to generate a file with all old sgd protein sequences

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 28, 2023Aug 28, 2023

• runoak_on_pombase

  Public
  runoak on PomBase data

  Shell

  •

  MIT License

  •0•0•0•0•Updated Aug 4, 2023Aug 4, 2023

• allele_gene_variant_features_regex

  Public
  Regular expression patterns for alllele variant features as described in the publication

  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 12, 2023Jul 12, 2023

• fypo_templates_spa

  Public
  A simple interface to create FYPO terms from templates

  HTML

  •

  MIT License

  •0•0•0•0•Updated Jun 28, 2023Jun 28, 2023

• create_pombase_spotlight

  Public
  Small web app to create the text for the spotlight and adapt the image size

  HTML

  •

  MIT License

  •0•0•0•0•Updated Apr 27, 2023Apr 27, 2023

• ncbi_submission

  Public
  Code for submitting the pombe genome to NCBI

  Python

  •

  MIT License

  •0•1•0•0•Updated Mar 9, 2023Mar 9, 2023

• goslims2gmt

  Public
  Extract genes associated to go slims and convert them to gmt format using PomBase API

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 24, 2023Jan 24, 2023

• jbrowse

  Public
  A modern genome browser built with JavaScript and HTML5.

  JavaScript

  •

  Other

  •198•0•0•0•Updated Jun 26, 2022Jun 26, 2022

• pombemine-bio-sources

  Public
  Java

  •1•0•0•0•Updated Jun 9, 2022Jun 9, 2022

• pombemine

  Public
  Java

  •1•0•0•0•Updated Jun 8, 2022Jun 8, 2022

• .github

  Public
  0•0•0•0•Updated Jan 6, 2022Jan 6, 2022

• pombase_rc_string

  Public
  A reference counted String class for PomBase

  Rust

  •

  MIT License

  •1•0•0•0•Updated Oct 22, 2021Oct 22, 2021