Repositories list

• msuefishlab.github.io

  Public
  HTML

  •

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

  •0•1•0•0•Updated Sep 11, 2024Sep 11, 2024

• rename_ensembl

  Public
  Script for Renaming Ensembl Genes Based on Prefixes

  0•1•0•0•Updated May 29, 2024May 29, 2024

• CircosAlignmentPlotter

  Public
  Converts a part of an alignment (.PAF perhaps others sometimes) to a Circos image using BED and fasta files.

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Dec 6, 2023Dec 6, 2023

• crotalus_rnaseq

  Public
  HTML

  •0•0•0•0•Updated Nov 13, 2023Nov 13, 2023

• msuefishslab_eorna

  Public
  The EORNA website is designed to store and visualize gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes within the barley genome.

  Perl

  •

  BSD 2-Clause "Simplified" License

  •1•0•0•0•Updated Sep 8, 2022Sep 8, 2022

• molec_evol_epdl2

  Public
  Shell

  •0•0•0•0•Updated Jul 12, 2022Jul 12, 2022

• msuefishlab_old

  Public
  HTML

  •0•0•0•0•Updated Dec 11, 2021Dec 11, 2021

• tdmsreader

  Public
  A LabVIEW tdms file reader

  R

  •

  GNU Lesser General Public License v3.0

  •3•6•5•0•Updated Mar 22, 2021Mar 22, 2021

• paramormyrops_rnaseq

  Public
  Analysis scripts and code for Paramormyrops RNA-seq project

  Shell

  •0•0•0•0•Updated Oct 17, 2020Oct 17, 2020

• picq_etal_genetic_drift_2020

  Public
  Code Associated with Picq et al. 2020 Evolution

  MATLAB

  •0•0•0•0•Updated Feb 28, 2020Feb 28, 2020

• data_download

  Public
  bash script to create and populate the data directories for efish comparative genomics work

  Shell

  •0•0•0•0•Updated Oct 24, 2019Oct 24, 2019

• eodrecorder2

  Public
  MATLAB Based EOD Recording Software

  MATLAB

  •0•0•12•0•Updated Jun 14, 2019Jun 14, 2019

• crisporWebsite

  Public
  All source code of the crispor.org website

  HTML

  •

  Other

  •43•0•0•0•Updated Mar 14, 2019Mar 14, 2019

• GenABEL

  Public
  ❗ This is a read-only mirror of the CRAN R package repository. GenABEL — genome-wide SNP association analysis. Homepage: http://www.genabel.org, http://forum.genabel.org,<U+000a>http://genabel.r-forge.r-project.org/ Report bugs for this package: http://r-forge.r-project.org/tracker/?group_id=505

  R

  •16•0•0•0•Updated Feb 26, 2019Feb 26, 2019

• orthofinder_tests

  Public
  bash and slurm scripts for initial tests on Orthofinder tool

  Shell

  •0•0•0•0•Updated Dec 3, 2018Dec 3, 2018

• miniBarcoder

  Public
  DNA barcoding using MinION

  Python

  •5•0•0•0•Updated Nov 6, 2018Nov 6, 2018

• SNPhylo

  Public
  A pipeline to generate a phylogenetic tree from huge SNP data

  Shell

  •

  GNU General Public License v2.0

  •38•0•0•0•Updated Oct 5, 2018Oct 5, 2018

• wustl_rnaseq

  Public
  Shell

  •0•0•0•0•Updated Aug 21, 2018Aug 21, 2018

• RATT-with-GFF

  Public
  RATT-with-GFF enables Rapid Annotation Transfer Tool (RATT) to be used with a GFF as your annotation file. RATT is a great tool for transferring annotations from one genome to another, but requires the annotations be in EMBL format. This pipeline is designed to use existing file conversion tools in order to run RATT with GFF annotations files

  Python

  •5•0•0•0•Updated Jun 21, 2018Jun 21, 2018

• trinity_singularity

  Public
  A Singularity File for Running Trinity on the HPCC

  1•0•0•0•Updated Jun 4, 2018Jun 4, 2018

• eodplotter

  Public
  A pipeline tool for EOD data

  HTML

  •1•0•0•1•Updated May 22, 2018May 22, 2018

• tdmsviewer

  Public
  Shiny app to view TDMS data

  R

  •1•2•3•0•Updated Mar 23, 2018Mar 23, 2018

• labview_eod_recorder

  Public
  Source Code for LabView EOD Recorders

  LabVIEW

  •0•0•0•0•Updated Mar 14, 2018Mar 14, 2018

• gatk_singularity

  Public
  Attempt at Docker/GATK Port to Singularity for MSU HPCC

  0•0•0•0•Updated Feb 26, 2018Feb 26, 2018

• garrulous-turtle

  Public
  workbook for assembly of the *Paramormyrops kingsleyae* genome

  Shell

  •1•0•0•0•Updated Feb 22, 2018Feb 22, 2018

• gatk4-data-processing

  Public
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

  WDL

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

  •77•0•0•0•Updated Jan 23, 2018Jan 23, 2018

• efishgenomics_expressiondb

  Public
  App for hosting gene expression/ontology data with Shiny

  R

  •7•0•0•0•Updated Jan 8, 2018Jan 8, 2018

• shinyorthologs

  Public
  Shiny app to look at orthologs

  Perl

  •0•0•9•0•Updated Aug 18, 2017Aug 18, 2017

• eod_viewer

  Public
  EOD file viewer using Shiny

  R

  •0•0•0•0•Updated Aug 17, 2017Aug 17, 2017

• EODBox

  Public
  Eagle

  •0•0•0•0•Updated May 26, 2016May 26, 2016