Pinned Repositories
branchwater-web
web app for search of SRA with Mastiff
GuideMaker
GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes
itsxpress
Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis
metagenomics
Tutorial for Metagenomics Analyses
Microbiome-workshop
2017 microbiome workshop website
micrompn
MicroMPN: A Python command line program for automating most probable number (MPN) estimates in microtiter plates
PanPipes
Test sets and pipeline scripts for pan-genomic graph analysis
q2_itsxpress
A plugin for qiime2 that runs ITSxpress
scinet-site
The SCINet website for the USDA-ARS
vica
Vica: Software to identify highly divergent DNA and RNA viruses and phages in microbiomes
USDA-ARS Genomics and Bioinformatics Research Unit's Repositories
USDA-ARS-GBRU/PanPipes
Test sets and pipeline scripts for pan-genomic graph analysis
USDA-ARS-GBRU/itsxpress
Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis
USDA-ARS-GBRU/GuideMaker
GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes
USDA-ARS-GBRU/q2_itsxpress
A plugin for qiime2 that runs ITSxpress
USDA-ARS-GBRU/QTLsurge
Software for iterative genotyping design in a QTL-seq experiment
USDA-ARS-GBRU/crossword
USDA-ARS-GBRU/Grass_annotation_pipeline
USDA-ARS-GBRU/branchwater-web
web app for search of SRA with Mastiff
USDA-ARS-GBRU/GEERU_workshop
thoe 2024 GEERU/MSU scoping workshop in Starkville, MS
USDA-ARS-GBRU/itsxpress-tutorial
A tutorial for the QIIME2 forum
USDA-ARS-GBRU/Ssec_Raleigh
Developing reference genome assembly for Stenotaphrum secundatum cultivar Raleigh
USDA-ARS-GBRU/tamipami
A tool for finding the TAM and PAM sites of new Cas and transposon endonucleases from NGS screens
USDA-ARS-GBRU/xmfa_tools
utilities for interacting with XMFA files
USDA-ARS-GBRU/audio-phenotyping-brapi-backend
BrAPI based API back-end for transferring audio and other log files to a Breedbase instance
USDA-ARS-GBRU/bioconda-recipes
Conda recipes for the bioconda channel.
USDA-ARS-GBRU/depthai-python
DepthAI Python Library
USDA-ARS-GBRU/DigitalPhenotyping
USDA-ARS-GBRU/FruitQuality
USDA-ARS-GBRU/ITS_HMMs
This is a versioned data collection containing a collection of HMMER models to identify the ends of ITS sequences.
USDA-ARS-GBRU/itsxpress-paper
Code supporting the paper "ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis"
USDA-ARS-GBRU/logomaker
Software for the visualization of sequence-function relationships
USDA-ARS-GBRU/meta_ML
Metagenomics machine learning project for retreat codathon
USDA-ARS-GBRU/MicroMPN_data-files
USDA-ARS-GBRU/Pepper_TrioBinning
USDA-ARS-GBRU/SalmoVar
Salmonella variant-calling pipeline
USDA-ARS-GBRU/seed-microbiome-traits
USDA-ARS-GBRU/sewrl_stinkbug_diet
A project to demultiplex and analize
USDA-ARS-GBRU/SugarcaneCrossingTool
USDA-ARS-GBRU/Wheat_Genome_Assembly
USDA-ARS-GBRU/Wheat_glaucousness_mapping