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applied_bioinformatics

The repository for the Spring 2019 iteration of Applied Bioinformatics. This semester will focus on teaching bioinformatics to undergrads using Nanopore sequencing to drive course projects.

applied_bioinformatics2020

Repository for BIO332 SP2020. Contains GitHub pages configuration, course notes, webpage tutorials, code, reading lists, and blog posts.

archaic

Exploration, clustering, visualization and classification of DNA damage patterns

bio331_2021

Notes and code for Bioinformatics 2021

bio331_geospatial

Geospatial lessons for BIO3331 -- Notes and R scripts

bioinformatics

An Introductory Undergraduate course in Bioinformatics

botany_oer

Open Educational Resources for BIO303 Environmental Botany

cerro_bayo

CRACLE analysis of Jurassic fossils

cracle

Finally an R package dedicated to the CRACLE method for estimating climate from biological proxies.

cracle_examples

cv19_enm

demo

Code demonstration pages

gbif_sql

A pipeline for building and maintaining a local SQL mirror of the Global Biodiversity Information Facility database in SQL. A local, optimized SQL database can increase data access speeds by several orders of magnitude.

geo_cuda

Experimental geographic manipulation functions adapted to GPU processing with CUDA.

intro_bioinformatics

A generalized version of an undergraduate introductory course in Bioinformatics

isoetes1

A methods testing pipeline for classification of short-read plant metagenomic data from environmental or ancient DNA

malthus

Exploratory analyses using Alpha Vantage financial API

meta_damage

Experimental pipeline for ancient DNA damage pattern detection in metagenomic samples.

neotoma_metabarcoding

neotomaseq

Packrat ancient DNA metagenomics pipeline and tools

oq2018_figure_code

R code and results files to create figures published in Harbert and Nixon, 2018 (Open Quaternary)

pmdtools

pylandsat

Python bulk landsat dowloads -- Adapted from geologyandpython.com tutorials

python_workshop

SICG Workshop -- Introduction to Python Programming for Bioinformatics

raster_pet

An R script for calculating the Thornthwaite Potential Evapotranspiration on global temperature raster layers

rasterextras

Towards a framework for parallel computing with raster and other geospatial data objects in R.

rsh249.github.io

public-page

sdm_modeltest

Testing data preprocessing and automation for SDMs using ENMeval and Maxent

semester-biology

spatial_bioinformatics

RGGS short course in spatial bioinformatics