rsh249

bioinformatics

An Introductory Undergraduate course in Bioinformatics

rasterExtras

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

bio331_2021

Notes and code for Bioinformatics 2021

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.

vegdistmod

R library for the analysis of spatial biodiversity data. Including tools to estimate climate from species coexistence including CRACLE and Thompson's Mutual Climatic Range technique.

cRacle

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

malthus

Exploratory analyses using Alpha Vantage financial API

pyLandsat

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

python_workshop

SICG Workshop -- Introduction to Python Programming for Bioinformatics

rsh249.github.io

public-page

semester-biology

bio331_geospatial

Geospatial lessons for BIO3331 -- Notes and R scripts

cracle_examples

cv19_enm

geo_cuda

Experimental geographic manipulation functions adapted to GPU processing with CUDA.

meta_damage

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

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)

sdm_modeltest

Testing data preprocessing and automation for SDMs using ENMeval and Maxent

stonehill_eDNA

Repository for processing metabarcoding data from our Stonehill aquatic eDNA project.

streetmap

Creating streetmap images using OSM data and *sometimes* landsat base layers

usgs_packrat_midden_db

Code to access the USGS packrat midden database with an archived version of the data

applied_bioinformatics2020

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

botany_OER

Open Educational Resources for BIO303 Environmental Botany

cerro_bayo

CRACLE analysis of Jurassic fossils

intro_bioinformatics

A generalized version of an undergraduate introductory course in Bioinformatics

neotoma_metabarcoding

PMDtools

testmerge

Experimenting with simple paired end read merging in R.

trajectory_demo