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

Dynamic Model

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

R package for the VRAP program

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

Code and scripts for the RNA-seq analysis of project: Deciphering the cellular roles and dissecting functional regions of UPF3A and UPF3B in human NMD

TUCCA's RNA-Seq Workflow for Read Quantification, Differential Expression, and Pathway Enrichment Analysis

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

Code and scripts for the RNA-seq analysis of project: SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity

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

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

DMVRAP shiny application

R package for VRAP rewrite

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

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

Density of juvenile salmon in Caithness rivers - R-shiny dashboard

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