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abhgenotyper

The ABHgenotypeR R package to easily visualize and manipulate ABH genotypes

ag2pi_gwas_workshop_june2021

ag2pi_snp_workshop_may2021

agriutilities

agro932-lab

computational lab for AGRO-932

agro932hw1

beanciat.github.io

WebPage

bioinformatics

bioinformatics_pipeline

Space for development of bioinformatic pipelines

cmplot

📊 Circular and Rectangular Manhattan Plot

computationalgenomicsmanual

Robs manual for the computational genomics and bioinformatics class.

cyverse_variant_analyses

Materials for CyVerse Variant Analyses course

earthengine-api

Python and JavaScript bindings for calling the Earth Engine API.

field-book

fieldhub

A Shiny App to Randomize Partially-Replicated/Unreplicated, Augmented, and Classical Field Designs for Plant Breeding Trials.

fieldimager.extra

Package with new tools to support FIELDimageR software on evaluating GIS images from agriculture field trials.

gapit3

Genome Association Predict Integrate Tools

gatk

Official code repository for GATK versions 4 and up

gbsprep

geospatialworkbook

Tutorials for the informatics on geographical information

gwaspoly

GWAS software that can handle autopolyploids

hos6236.github.io

Website: HOS 6236 Molecular Marker Assisted Plant Breeding

ilci-nirs-workshop-2024

itai

Data analysis of the Itai site to create Figure 1 for class project

lfelipe-ferrao.github.io

My personal website

metan

Package for multi-environment trial analysis

mrbeanapp

Web application V.0.2

ngsepcore

NGSEP is an integrated framework for analysis of high throughput sequencing (HTS) reads. The main functionality of NGSEP is the variants detector, which allows to make integrated discovery and genotyping of Single Nucleotide Variants (SNVs), insertions, deletions, and genomic regions with copy number variation (CNVs).

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.