Repositories list

• iSciComp

  Public
  JupyterBook: Introduction to Scientific Computation

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

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

• emevo

  Public
  Simluate Embodied Evolution of Agents

  Jupyter Notebook

  •

  Apache License 2.0

  •0•2•0•0•Updated Nov 16, 2024Nov 16, 2024

• BioinfoUgrp

  Public
  OIST Bioinfo user group

  hpcoistbioinformatics

  Shell

  •2•7•1•0•Updated Nov 2, 2024Nov 2, 2024

• LuscombeU_stlpreprocess

  Public
  Download and pre-process genomes for the Scrambling in the Tree of Life project

  genomedownloadfilter+ 2scramblingoist

  Nextflow

  •

  MIT License

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

• plessy_pairwiseGenomeComparison

  Public
  Draft workflow for pairwise genome comparison. We recommend you use the new nf-core version instead: https://nf-cor.e/pairgenomealign

  bioinformaticsgenomicsnextflow+ 2comparative-genomicswhole-genome-alignment

  Nextflow

  •3•4•2•0•Updated Nov 1, 2024Nov 1, 2024

• VisualStimulation

  Public
  matlab gui for vstim with psychophysics toolbox

  Jupyter Notebook

  •0•1•0•0•Updated Oct 24, 2024Oct 24, 2024

• iridophore-automeasure

  Public
  Python code for automated measuring of iridophore crystals from TEM images

  Python

  •0•0•0•0•Updated Oct 23, 2024Oct 23, 2024

• LuscombeU_annotationpolish

  Public
  R package for annotation polishing

  R

  •0•1•1•0•Updated Oct 18, 2024Oct 18, 2024

• LuscombeU_nfcore_pairgenomealign_fork

  Public
  Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

  Nextflow

  •

  MIT License

  •2•0•0•0•Updated Oct 15, 2024Oct 15, 2024

• LuscombeU_stlrepeatmask

  Public
  Mask genomic repeats and low-complexity regions for the Scrambling in the Tree of Life project

  genomerepeatsscrambling+ 2maskingoist

  Nextflow

  •

  MIT License

  •1•0•0•0•Updated Oct 10, 2024Oct 10, 2024

• DigitalBrain

  Public
  Digital Brain Project

  0•0•0•0•Updated Sep 21, 2024Sep 21, 2024

• BioinfoUgrp_UnixGoodies_Images

  Public
  Singularity images with cool Unix tools to be exported as modules in HPC clusters

  Dockerfile

  •0•3•2•0•Updated Sep 13, 2024Sep 13, 2024

• smartphone-robot-android

  Public
  Android development for smartphone-robot

  Java

  •0•0•1•1•Updated Sep 4, 2024Sep 4, 2024

• replifactory_v7

  Public archive
  JavaScript

  •2•0•2•0•Updated Sep 2, 2024Sep 2, 2024

• groups-static-upstream

  Public
  0•0•0•0•Updated Aug 28, 2024Aug 28, 2024

• BrainComputation

  Public
  Brain Computation: A Hands-on Guidebook

  Jupyter Notebook

  •0•2•0•0•Updated Aug 20, 2024Aug 20, 2024

• TER-UCE-DB

  Public
  The Termite UCE Database. Centralization of termite UCE data and assignation of unique identification code.

  Other

  •2•3•0•0•Updated Aug 15, 2024Aug 15, 2024

• smartphone-robot-object-detection

  Public
  Images and bounding box data set and code for generating tflite models

  Python

  •0•0•0•0•Updated Aug 9, 2024Aug 9, 2024

• optinist

  Public
  calcium imaging pipeline tool

  neurosciencecalcium-imaging

  TypeScript

  •

  GNU General Public License v3.0

  •13•37•50•8•Updated Aug 8, 2024Aug 8, 2024

• GenomicBreaks

  Public
  Pairwise Alignment Breakpoint Analysis

  comparative-genomicsr

  R

  •

  Other

  •3•4•18•0•Updated Aug 5, 2024Aug 5, 2024

• optinist_tutorial_preparation

  Public
  Information for preparation of the hands-on tutorial for optinist

  0•0•0•0•Updated Jul 4, 2024Jul 4, 2024

• LuscombeU_changchang

  Public
  Analyse tandem repeats (draft)

  R

  •0•0•0•0•Updated Jun 25, 2024Jun 25, 2024

• OCNC_tutorial_optinist

  Public
  0•0•0•0•Updated Jun 16, 2024Jun 16, 2024

• Oikopleuradioica_genomeannotation

  Public
  Genome annotation of Oikopleura dioica from different geographical locations

  Shell

  •0•1•1•0•Updated Jun 5, 2024Jun 5, 2024

• LuscombeU-CAGE_libraries

  Public
  Quality control and processing of CAGE libraries

  Shell

  •1•2•0•0•Updated May 17, 2024May 17, 2024

• LaTeX-template-phd-thesis-proposal

  Public archive
  LaTeX Template for OIST PhD Thesis Proposal

  TeX

  •

  MIT License

  •7•1•0•1•Updated May 16, 2024May 16, 2024

• LaTeX-template-phd-thesis

  Public archive
  LaTeX Template for OIST Thesis

  TeX

  •

  MIT License

  •2•2•0•1•Updated May 16, 2024May 16, 2024

• plessy_Presentation_2024_OIST-CNRS

  Public
  Poster presented at the 2024 OIST-CNRS Joint Symposium on West Pacific Marine Biology

  HTML

  •0•0•0•0•Updated Apr 26, 2024Apr 26, 2024

• plessy_nf_GenomicBreaks

  Public
  Draft Nextflow pipeline to convert alignment files and extract basic stats.

  Nextflow

  •0•0•0•0•Updated Apr 19, 2024Apr 19, 2024

• plessy_oikgenomes_drat

  Public
  Drat repository for hosting oik BSgenome packages

  rbsgenomeoikopleura

  0•0•0•0•Updated Apr 18, 2024Apr 18, 2024