Repositories list

• spatial

  Public
  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated May 24, 2023May 24, 2023

• G606_Phylogenetics

  Public
  For Gen606 Phylogenetics lesson

  Creative Commons Zero v1.0 Universal

  •1•0•0•0•Updated May 3, 2023May 3, 2023

• DoveParentsRNAseq

  Public
  Characterizing the neurogenomics of parental care in the rock dove

  R

  •2•5•6•0•Updated Dec 29, 2021Dec 29, 2021

• Oyster_River_Protocol

  Public
  Official Repository of the Oyster River Protocol for Transcriptome Assembly

  genomicsassemblyrnaseq+ 2transcriptome-assemblyoyster-river-protocol

  TeX

  •

  Creative Commons Zero v1.0 Universal

  •14•16•23•4•Updated Aug 12, 2021Aug 12, 2021

• orp_website

  Public
  Website for Oyster River Protocol

  Creative Commons Zero v1.0 Universal

  •1•3•0•0•Updated Apr 22, 2021Apr 22, 2021

• driftR

  Public
  population genetic simulations with R and Shiny

  R

  •9•0•0•0•Updated Nov 17, 2020Nov 17, 2020

• dnazoo_annotation

  Public
  This is the code to reproduce the DNAzoo genome annotations.

  Shell

  •

  GNU General Public License v3.0

  •1•1•1•0•Updated Jul 7, 2020Jul 7, 2020

• pecr_genome

  Public
  Files used for pecr genome

  Shell

  •

  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated May 27, 2020May 27, 2020

• HackMD

  Public
  HackMD notes

  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated Mar 26, 2020Mar 26, 2020

• OrthoFinder

  Public
  Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"

  Python

  •

  GNU General Public License v3.0

  •189•1•0•0•Updated Jan 7, 2020Jan 7, 2020

• EMBL_Workshop

  Public
  Materials for the EMBL-EBI workshop

  0•1•0•0•Updated Oct 4, 2019Oct 4, 2019

• museum_genomics

  Public
  This is the repo for the Museum Genomics Paper

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

  •0•0•0•0•Updated Jul 25, 2019Jul 25, 2019

• MCBS913_2019

  Public
  This is the repo for the Spring 2019 version of MCBS913

  machine-learningbioinformaticsgenomics+ 3metagenomicsalignmentminhash

  Python

  •

  The Unlicense

  •1•1•0•0•Updated May 22, 2019May 22, 2019

• phylotator

  Public
  Phylotator is software for using ideas from phylogenetics to annotate transcripts

  Makefile

  •

  MIT License

  •0•0•0•0•Updated Apr 23, 2019Apr 23, 2019

• Dockerfiles

  Public
  docker files

  Mozilla Public License 2.0

  •0•0•0•0•Updated Mar 27, 2019Mar 27, 2019

• nhen

  Public
  Nhen's stuff

  researchundergrad

  Python

  •0•0•0•0•Updated Mar 22, 2019Mar 22, 2019

• RockDove

  Public
  NSF Funded Project with Rebecca Calisi

  Creative Commons Zero v1.0 Universal

  •2•0•0•0•Updated Mar 13, 2019Mar 13, 2019

• XSEDE18

  Public
  2018 Xsede application

  TeX

  •0•0•0•0•Updated Apr 12, 2018Apr 12, 2018

• Umea_Workshop

  Public
  Materials for the Umea Workshop

  Mozilla Public License 2.0

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

• Shannon

  Public
  RNA-Seq

  Python

  •13•0•0•0•Updated Mar 9, 2018Mar 9, 2018

• kmers_as_metrics

  Public
  Can you use kmers to evaluate transcriptiome assemblies

  MIT License

  •0•0•0•0•Updated Mar 1, 2018Mar 1, 2018

• transrate

  Public
  Understand your transcriptome assembly

  Ruby

  •

  Other

  •34•0•0•0•Updated Aug 8, 2017Aug 8, 2017

• testesDGE

  Public
  files for Laurens DGE paper

  MIT License

  •0•1•1•0•Updated May 16, 2017May 16, 2017

• Lauren

  Public
  0•0•0•0•Updated May 16, 2017May 16, 2017

• peer_rnaseq

  Public
  PEER RNA seq manuscript

  MIT License

  •0•1•0•0•Updated Mar 22, 2017Mar 22, 2017

• general

  Public
  general code

  Shell

  •

  MIT License

  •4•2•0•3•Updated Oct 18, 2016Oct 18, 2016

• sequencetools

  Public
  Set of scripts etc. to work with DNA sequence and related files

  Perl

  •

  The Unlicense

  •7•0•0•0•Updated Sep 7, 2016Sep 7, 2016

• tuco_manuscript

  Public
  AL Tuco Manuscript Code

  MIT License

  •1•0•0•0•Updated Aug 26, 2016Aug 26, 2016

• peer_reproductive-transcriptome

  Public
  for manuscript

  Creative Commons Zero v1.0 Universal

  •0•0•1•0•Updated Aug 23, 2016Aug 23, 2016

• Gen711

  Public
  3•12•1•0•Updated Aug 16, 2016Aug 16, 2016