Repositories list

• Grass_annotation_pipeline

  Public
  0•3•0•0•Updated Aug 4, 2025Aug 4, 2025

• HT-PAMDA

  Public
  Analysis pipeline for CRISPR high-throughput PAM determination assay (HT-PAMDA) data

  Python

  •

  GNU General Public License v3.0

  •6•0•0•0•Updated Aug 4, 2025Aug 4, 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•0•0•Updated Aug 1, 2025Aug 1, 2025

• Spectra

  Public
  Whole chromosome visualization tool

  Python

  •0•1•0•0•Updated Jul 10, 2025Jul 10, 2025

• SugarcaneCrossingTool

  Public
  R

  •1•0•4•0•Updated Jun 30, 2025Jun 30, 2025

• Cotton_CottonLeafCurlVirus_QTLmapping

  Public
  R

  •1•0•0•0•Updated Jun 3, 2025Jun 3, 2025

• digit_reading

  Public
  A library display and capture seven-segment display images to train machine learning models line EasyOCR

  Python

  •0•0•0•0•Updated May 6, 2025May 6, 2025

• branchwater-web-MAGtest

  Public
  Codes and notes associated with testing branchwater-web by creating MAGs of 5 Refseq search results.

  Nextflow

  •0•0•0•0•Updated Apr 29, 2025Apr 29, 2025

• sewrl_stinkbug_diet

  Public
  A project to demultiplex and analize

  Shell

  •0•0•0•0•Updated Apr 25, 2025Apr 25, 2025

• or_primers

  Public
  Prototype for using Mixed Integer Linear Programming to optimize multiplex primers

  Python

  •0•0•0•0•Updated Apr 2, 2025Apr 2, 2025

• itsxpress

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

  Python

  •

  Other

  •11•14•2•0•Updated Mar 26, 2025Mar 26, 2025

• cep_optimizer

  Public
  A mixed integer linear programming solution to FNS CEP programs

  Python

  •0•0•0•0•Updated Mar 25, 2025Mar 25, 2025

• StandardizedHeterozygosityEvaluation

  Public
  Shell

  •0•0•0•0•Updated Mar 10, 2025Mar 10, 2025

• seed-microbiome-traits

  Public
  R

  •0•0•0•0•Updated Mar 10, 2025Mar 10, 2025

• SalmoVar

  Public
  Salmonella variant-calling pipeline

  MIT License

  •1•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• PanPipes

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

  Python

  •2•17•0•0•Updated Jan 30, 2025Jan 30, 2025

• logomaker

  Public
  Software for the visualization of sequence-function relationships

  Jupyter Notebook

  •

  MIT License

  •42•0•0•0•Updated Jan 2, 2025Jan 2, 2025

• QTLsurge

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

  Perl

  •

  MIT License

  •1•5•1•0•Updated Dec 2, 2024Dec 2, 2024

• crossword

  Public
  R

  •2•4•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

• ITS_HMMs

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

  0•1•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

  •4•10•3•7•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

  •3.6k•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