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aas

Code to accompany Advanced Analytics with Spark from O'Reilly Media

aboutrmarkdown

A short tutorial to learn about R Markdown

alfie

A neural network for alignment-free, kingdom-level classification of eDNA

aphid

Analysis with Profile Hidden Markov Models

bigquery_helper

Helper class to simplify common read-only BigQuery tasks.

bioconda-recipes

Conda recipes for the bioconda channel.

blog_posts

bold-cli

Command line interface for the retrieval of data from http://www.boldsystems.org

brrr

Rap adlibs in R.

chromosome-plot

example code for visualizing genome wide data using ggplot

coil

An R package for pre-processing and error evaluation of COI-5P barcode data

ctci-6th-edition-python

Cracking the Coding Interview 6th Ed. Python Solutions

data-alfie

labelled COI-5P barcode data used in training alfie

debar

A sequence-by-sequence denoiser for COI DNA barcode and metabarcode data

dev-env

devo_integration_paper

email-report

A modular template for scraping data from the web to send yourself scheduled email reports

euler-solutions

my solutions to the problems at projecteuler.net, mix of go and python

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

fast-kmer

Take a fasta file and generate a tidy data frame with kmer count data

gene_region

Identifying gene regions associated with SNPs of interest

go-fasta

A tool for manipulating fasta files and obtaining new sequence data from NCBI in fasta format

golang-practice

Small go coding problems I do to stay in practice

hap.py

Haplotype VCF comparison tools

hidden_markov

Implementation of the Hidden Markov Model

hmm_docs

hugo-academic

📝 The website builder for Hugo. Build and deploy a beautiful website in minutes!

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

kaggle-code

A repository for some of the code I used in kaggle data science & machine learning tasks.