Repositories list

• itsxpress

  Public
  Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis

  Python

  •

  Other

  •9•12•0•0•Updated Jan 10, 2025Jan 10, 2025

• SugarcaneCrossingTool

  Public
  R

  •0•0•4•0•Updated Jan 9, 2025Jan 9, 2025

• tamipami

  Public
  A tool for finding the TAM and PAM sites of new Cas and transposon endonucleases from NGS screens

  Python

  •

  Other

  •1•1•1•0•Updated Jan 9, 2025Jan 9, 2025

• seed-microbiome-traits

  Public
  R

  •0•0•0•0•Updated Jan 7, 2025Jan 7, 2025

• logomaker

  Public
  Software for the visualization of sequence-function relationships

  Jupyter Notebook

  •

  MIT License

  •37•0•0•0•Updated Jan 2, 2025Jan 2, 2025

• sewrl_stinkbug_diet

  Public
  A project to demultiplex and analize

  Shell

  •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

• QTLsurge

  Public
  Software for iterative genotyping design in a QTL-seq experiment

  Perl

  •

  MIT License

  •1•4•1•0•Updated Dec 2, 2024Dec 2, 2024

• SalmoVar

  Public
  Salmonella variant-calling pipeline

  MIT License

  •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

• crossword

  Public
  R

  •2•3•4•0•Updated Oct 9, 2024Oct 9, 2024

• Pepper_TrioBinning

  Public
  Other

  •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

• Wheat_glaucousness_mapping

  Public
  R

  •0•0•0•0•Updated Sep 9, 2024Sep 9, 2024

• PanPipes

  Public
  Test sets and pipeline scripts for pan-genomic graph analysis

  Python

  •2•16•0•0•Updated Aug 22, 2024Aug 22, 2024

• ITS_HMMs

  Public
  This is a versioned data collection containing a collection of HMMER models to identify the ends of ITS sequences.

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

• GuideMaker

  Public
  GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes

  microbiologycrispr-casguidemaker

  Python

  •

  Other

  •3•7•1•6•Updated Jul 9, 2024Jul 9, 2024

• GEERU_workshop

  Public
  thoe 2024 GEERU/MSU scoping workshop in Starkville, MS

  0•2•0•0•Updated May 22, 2024May 22, 2024

• DigitalPhenotyping

  Public
  Jupyter Notebook

  •0•0•0•0•Updated May 7, 2024May 7, 2024

• FruitQuality

  Public
  Jupyter Notebook

  •0•0•0•0•Updated May 3, 2024May 3, 2024

• itsxpress-tutorial

  Public
  A tutorial for the QIIME2 forum

  1•2•1•0•Updated Apr 15, 2024Apr 15, 2024

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.3k•0•0•0•Updated Mar 21, 2024Mar 21, 2024

• itsxpress-paper

  Public
  Code supporting the paper "ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis"

  Shell

  •

  Other

  •0•0•0•0•Updated Feb 21, 2024Feb 21, 2024

• Wheat_Genome_Assembly

  Public
  0•0•0•0•Updated Feb 5, 2024Feb 5, 2024

• audio-phenotyping-brapi-backend

  Public
  BrAPI based API back-end for transferring audio and other log files to a Breedbase instance

  brapibreedbasebrapi-phenotyping

  JavaScript

  •1•0•0•0•Updated Feb 2, 2024Feb 2, 2024

• depthai-python

  Public
  DepthAI Python Library

  C++

  •

  MIT License

  •193•0•0•0•Updated Jan 22, 2024Jan 22, 2024

• branchwater-web

  Public
  web app for search of SRA with Mastiff

  HTML

  •0•2•0•0•Updated Jan 21, 2024Jan 21, 2024

• MicroMPN_data-files

  Public
  Jupyter Notebook

  •

  Other

  •1•0•0•0•Updated Jan 2, 2024Jan 2, 2024

• q2_itsxpress

  Public archive
  A plugin for qiime2 that runs ITSxpress

  Python

  •

  Other

  •5•7•4•0•Updated Dec 19, 2023Dec 19, 2023

• Grass_annotation_pipeline

  Public
  Shell

  •0•3•0•0•Updated Oct 4, 2023Oct 4, 2023

• Ssec_Raleigh

  Public
  Developing reference genome assembly for Stenotaphrum secundatum cultivar Raleigh

  Shell

  •0•1•0•0•Updated Sep 1, 2023Sep 1, 2023

• meta_ML

  Public
  Metagenomics machine learning project for retreat codathon

  Jupyter Notebook

  •0•0•0•0•Updated Aug 24, 2023Aug 24, 2023

• xmfa_tools

  Public
  utilities for interacting with XMFA files

  Perl

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Jul 28, 2023Jul 28, 2023