Cam Nugent's repositories
kaggle-code
A repository for some of the code I used in kaggle data science & machine learning tasks.
email-report
A modular template for scraping data from the web to send yourself scheduled email reports
py-morse-code
A morse code class for translation between morse and alphanumeric encodings, which supports text and audio message representation
snp-placer
Take information about snps on short sequence reads and accurately place the snps in a reference genome
salmon-genomic-vulnerability
Associating genomic variation with environment
hugo-academic
đź“ť The website builder for Hugo. Build and deploy a beautiful website in minutes!
lowdepth-2-snps
A bioinformatics pipeline to process low depth re-sequencing data and produce SNP calls and genotype likelihoods
RedfishAmpliconPipe
A snakemake pipeline for processing of redfish amplicon data
SalmonEuAdmix
A machine learning-based library for estimating European admixture proportions in Atlantic salmon
bioconda-recipes
Conda recipes for the bioconda channel.
data-alfie
labelled COI-5P barcode data used in training alfie
F19_ExploratoryAnalyses
This is one set of exploratory data analyses that can be used to look at data sets initially. Please feel free to contribute to this repository if you would like to add your own methods of exploratory analyses
Gene_region
Identifying gene regions associated with SNPs of interest
hap.py
Haplotype VCF comparison tools
hidden_markov
Implementation of the Hidden Markov Model
imputed-data-dynamic-threshold
Compute imputed variant exclusion lists based on https://doi.org/10.1002%2Fgepi.21603
IonTorrent-error-profiling
Code for the analysis of the error profile of IonTorrent sequencing data
sb-slurm
Snakemake profile for running on AWS ParallelCluster with the Slurm scheduler
update-salmon-220k-positions
Orient the SNPs from the Atlantic salmon 220K chip in v3 of the Atlantic salmon genome