Walks through installation and usage of FASTQC, MultiQC, Trimmomatic, and Salmon for transcriptomic data preprocessing. Includes Grid Engine shell scripts that can be looped over many files in a directory.

Repository for bulk RNA-seq analyses (from undergrad 2nd-3rd year) – Reorganized

R package for the VRAP program

Some information about whether the log-normal correction should be used in escapement goal analysis.

Code, data, and figures for an experimental pathogen exposure study using wood frogs and American bullfrogs

Dynamic Model

Datasets and related knowledge from the International Year of the Salmon (IYS) "Salmon Status and Trends" workshops

Snakemake workflow for Bulk RNASeq at both genome level and transcripts level.

R package for VRAP rewrite

DMVRAP shiny application

Analysis of Salmo trutta gametes and embryo microbiome project in Vals/Trun, Switzerland

Scripts accompanying manuscript "The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid"

Code to assess the state of Pacific salmon spawner abundance monitoring in Canada

Functions to explore, analyze, and visualize open data about salmon.

Datasets and related knowledge from the IYS Salmon Status and Trends workshops

Data from a longterm sea lice monitoring in the Broughton Archipelago, British Columbia, Canada by Alexandra Morton (Raincoast Research) and the Salmon Coast Field Station (salmoncoast.org)

Bioc2022 workshop. SEESAW: Statistical Estimation Of Allelic Expression Using Salmon And Swish

This is an R package that runs the standardized trends metrics used in the 5-year Viability Reports for listed PNW salmonids.