Pinned Repositories
BioinfoContainers
Various Singularity recipes I've used to generate containers
CP-NAM
Scripts used to process the Sorghum Carbon-Partitioning NAM
CP-NAM_2021
Dissecting the Genetic Architecture of Carbon Partitioning in Sorghum using Multiscale Phenotypes
features_from_snps
A python script for designed to find any genomic features (genes, CDS, etc) near SNPs or arbitrary coordinates
genotype_phenotype_boxplots
A tool for rapidly generating swarmplots and boxplots for phenotypes across genotypes from a gzipped VCF.
jlboat.github.io
My GitHub Pages site
NextflowScripts
Misc. Nextflow scripts
SAP_WGS
Whole-genome sequencing of the Sorghum Asssociation Panel
StatisticalGeneticsOfQuantitativeTraits
Associated scripts for the book by Rongling Wu, Chang-Xing Ma, and George Casella
vcf_to_hapmap
Convert large gzipped VCF to double-bit HapMap format
jlboat's Repositories
jlboat/BioinfoContainers
Various Singularity recipes I've used to generate containers
jlboat/SAP_WGS
Whole-genome sequencing of the Sorghum Asssociation Panel
jlboat/features_from_snps
A python script for designed to find any genomic features (genes, CDS, etc) near SNPs or arbitrary coordinates
jlboat/genotype_phenotype_boxplots
A tool for rapidly generating swarmplots and boxplots for phenotypes across genotypes from a gzipped VCF.
jlboat/StatisticalGeneticsOfQuantitativeTraits
Associated scripts for the book by Rongling Wu, Chang-Xing Ma, and George Casella
jlboat/vcf_to_hapmap
Convert large gzipped VCF to double-bit HapMap format
jlboat/beagle
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
jlboat/CP-NAM
Scripts used to process the Sorghum Carbon-Partitioning NAM
jlboat/CP-NAM_2021
Dissecting the Genetic Architecture of Carbon Partitioning in Sorghum using Multiscale Phenotypes
jlboat/PHENIX
A multiple phenotype imputation method for genetic studies
jlboat/StatisticalDesign
Scripts and data from George Casella's Statistical Design
jlboat/BayesASE
Bayesian analysis of allele specific expression
jlboat/jlboat.github.io
My GitHub Pages site
jlboat/BGPWAS
A sparse Bayesian Genome-Phenome Wide Association Study model
jlboat/Cromwell_PBSPro
An example implementation for the Cromwell workflow management system on PBS Pro
jlboat/DarkRegionFinder
jlboat/FastaUtils
Simple Java-based library for working with FASTA files
jlboat/Fuyin
福音
jlboat/grand_exchange
Generate files using variable lists -- originally desiged for PBS Pro QSUBs
jlboat/hapmap_to_qtl2
Convert HapMap file into a useable R qtl2 genotype file
jlboat/HMMSplicer
An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets
jlboat/jlboat
Personal description repository
jlboat/multiparent_percentages
Assess unique parental contribution to multiparent RILs
jlboat/que
A python script for checking a PBS Pro Job Scheduler queue
jlboat/query_qtl_atlas
This script was designed to find any QTLs near SNPs in the Sorghum QTL Atlas
jlboat/Robust-HSE-Examples
A robust methodology for assessing homoeolog-specific expression
jlboat/SorghumMagic
Scripts and methods used to analyze the Sorghum MAGIC population
jlboat/StarchProtein
Association and gene network analysis for starch and protein content in sorghum
jlboat/Tragopogon_castellanus
jlboat/VGTool
A tool for modelling graphs of genetic variation.