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
Some information about whether the log-normal correction should be used in escapement goal analysis.
Jupyter notebooks for DGE results and ontology analysis and visualisation.
Code, data, and figures for an experimental pathogen exposure study using wood frogs and American bullfrogs
Population genetics using microsatellites for different salmonid species
Simple Nextflow RNA-Seq pipeline
First Get Coding Project: 2d top-down game. Player is a salmon swimming up river avoiding obstacles along the way.
Python client for the CAX API. Holmes, E. E and M. Williams. 2023. pycax: a Python client for the Coordinated Assessments data exchange REST API
Fulfills a data request to estimate sport fish harvest in the Upper Cook Inlet Exclusive Economic Zone.
Reproducible RNA-seq analysis (Salmon, tximport, DESeq2) — mouse dataset from Johns Hopkins Coursera course
RNA-seq analysis from FASTQ to differential gene-expression using open-source tools
Add a description, image, and links to the salmon topic page so that developers can more easily learn about it.
To associate your repository with the salmon topic, visit your repo's landing page and select "manage topics."