Repositories list

• pire_stethojulis_interrupta_lcwgs

  Public
  Analysis of low-coverage whole genome sequencing data from Stethojulis interrupta

  HTML

  •0•2•0•0•Updated Feb 11, 2025Feb 11, 2025

• pire_sphaeramia_orbicularis_lcwgs

  Public
  Analysis of low-coverage whole genome sequencing data from Sphaeramia orbicularis

  HTML

  •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

• pire_zenarchopterus_dispar_lcwgs

  Public
  Analysis of low-coverage whole genome sequencing data from Zenarchopterus dispar

  HTML

  •0•1•0•0•Updated Jan 30, 2025Jan 30, 2025

• pire_ssl_data_processing

  Public
  SHOTGUN DATA PROCESSING & ANALYSIS

  HTML

  •

  MIT License

  •1•0•0•0•Updated Dec 10, 2024Dec 10, 2024

• pire_fq_gz_processing

  Public
  Pre-Processing PIRE Data

  Shell

  •

  MIT License

  •2•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• pire_taeniamia_zosterophora_lcwgs

  Public
  Repository for bioinformatics and analysis of historical and contemporary low-coverage whole genome sequencing data of Taeniamia zosterophora collected in the Philippines.

  HTML

  •0•1•0•0•Updated Nov 14, 2024Nov 14, 2024

• pire_cssl_data_processing

  Public
  HTML

  •1•0•3•0•Updated Oct 28, 2024Oct 28, 2024

• fish_biodiversity

  Public
  R

  •0•0•15•0•Updated Jul 4, 2024Jul 4, 2024

• enzyme_inhibition_in_museum_fishes

  Public
  R

  •0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

• ptaPIRE

  Public
  Multispecies analysis of joint site frequency spectra with PTA

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Feb 28, 2024Feb 28, 2024

• Welcome-README

  Public
  More info and news

  0•0•0•0•Updated Jan 30, 2024Jan 30, 2024

• 2022_PIRE_omics_workshop

  Public
  HTML

  •1•0•0•0•Updated Jan 22, 2024Jan 22, 2024

• REUs

  Public
  As part of the "Research Experience for Undergraduates" component, our student conduct independent research projects. Find out more about their research here.

  0•0•0•0•Updated Feb 16, 2023Feb 16, 2023

• PIRE_TemporalSims_HPC

  Public
  Scripts for simulating recent demographic declines (written for Rutgers' Amarel cluster)

  Python

  •0•1•0•0•Updated Oct 24, 2022Oct 24, 2022

• 2022_PIRE_R_workshop

  Public
  This repository was created separate from the 2022_PIRE_omics_workshop repository to make it easier for attendees to clone workshop materials locally

  R

  •0•0•0•0•Updated Jul 18, 2022Jul 18, 2022

• PIRE_Virtual_Workshop

  Public
  The purpose of this repository is to instruct biologists in Regular expressions, basic UNIX, how to interface with the Old Dominion University High Performance Computing Cluster, how to execute SLURM commands and how to use Git and GitHub.

  Rich Text Format

  •0•0•0•0•Updated Jun 23, 2022Jun 23, 2022

• scripts_and_code

  Public
  Shell

  •0•0•0•0•Updated Jun 5, 2021Jun 5, 2021

• PIRE_Temporal_Sims

  Public
  Simulation and analysis scripts for quantifying power to detect recent declines from temporal genomic data

  Python

  •0•0•0•0•Updated Dec 22, 2020Dec 22, 2020

• PIRE_momi2_simulation

  Public
  Code for simulating recent demographic change (via msprime) and evaluating power and accuracy to detect various demographic changes (using momi2)

  Jupyter Notebook

  •0•0•0•0•Updated Nov 3, 2020Nov 3, 2020

• CarpenterLabPythonWorkshop

  Public
  This repository contains the materials for the summer 2020 Carpenter Lab Python Workshop.

  Python

  •1•0•0•0•Updated Jul 26, 2020Jul 26, 2020

• GenomicsWorkshop

  Public
  Materials from our free genomics workshop at Silliman University, Dumaguete, Philippines.

  R

  •0•0•0•0•Updated Sep 2, 2019Sep 2, 2019