Pinned Repositories
alfie
A neural network for alignment-free, kingdom-level classification of eDNA
coil
An R package for pre-processing and error evaluation of COI-5P barcode data
debar
A sequence-by-sequence denoiser for COI DNA barcode and metabarcode data
email-report
A modular template for scraping data from the web to send yourself scheduled email reports
golang-practice
Small go coding problems I do to stay in practice
kaggle-code
A repository for some of the code I used in kaggle data science & machine learning tasks.
py-morse-code
A morse code class for translation between morse and alphanumeric encodings, which supports text and audio message representation
RedfishAmpliconPipe
A snakemake pipeline for processing of redfish amplicon data
SalmonEuAdmix
A machine learning-based library for estimating European admixture proportions in Atlantic salmon
CNuge's Repositories
CNuge/kaggle-code
A repository for some of the code I used in kaggle data science & machine learning tasks.
CNuge/email-report
A modular template for scraping data from the web to send yourself scheduled email reports
CNuge/alfie
A neural network for alignment-free, kingdom-level classification of eDNA
CNuge/py-morse-code
A morse code class for translation between morse and alphanumeric encodings, which supports text and audio message representation
CNuge/snp-placer
Take information about snps on short sequence reads and accurately place the snps in a reference genome
CNuge/coil
An R package for pre-processing and error evaluation of COI-5P barcode data
CNuge/lowdepth-2-snps
A bioinformatics pipeline to process low depth re-sequencing data and produce SNP calls and genotype likelihoods
CNuge/salmon-genomic-vulnerability
Associating genomic variation with environment
CNuge/UGRU
2018-2020 University of Guelph R Users Group Code
CNuge/BOLD-CLI
Command line interface for the retrieval of data from http://www.boldsystems.org
CNuge/debar
A sequence-by-sequence denoiser for COI DNA barcode and metabarcode data
CNuge/hugo-academic
📝 The website builder for Hugo. Build and deploy a beautiful website in minutes!
CNuge/RedfishAmpliconPipe
A snakemake pipeline for processing of redfish amplicon data
CNuge/SalmonEuAdmix
A machine learning-based library for estimating European admixture proportions in Atlantic salmon
CNuge/aphid
Analysis with Profile Hidden Markov Models
CNuge/bioconda-recipes
Conda recipes for the bioconda channel.
CNuge/blog_posts
CNuge/data-alfie
labelled COI-5P barcode data used in training alfie
CNuge/dev-env
CNuge/Devo_integration_paper
CNuge/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
CNuge/fast-kmer
Take a fasta file and generate a tidy data frame with kmer count data
CNuge/Gene_region
Identifying gene regions associated with SNPs of interest
CNuge/hap.py
Haplotype VCF comparison tools
CNuge/hidden_markov
Implementation of the Hidden Markov Model
CNuge/imputed-data-dynamic-threshold
Compute imputed variant exclusion lists based on https://doi.org/10.1002%2Fgepi.21603
CNuge/IonTorrent-error-profiling
Code for the analysis of the error profile of IonTorrent sequencing data
CNuge/sb-slurm
Snakemake profile for running on AWS ParallelCluster with the Slurm scheduler
CNuge/update-salmon-220k-positions
Orient the SNPs from the Atlantic salmon 220K chip in v3 of the Atlantic salmon genome
CNuge/W2020
Tutorials and code for the winter 2020 semester