schmitzlab's repositories
Widespread-Long-range-Cis-Regulatory-Elements-in-the-Maize-Genome
scripts used for processing and analyzing data in the article.
The-prevalence-evolution-and-chromatin-signatures-of-plant-regulatory-elements
Scripts used for processing and analyzing data in the article "The prevalence, evolution and chromatin signatures of plant regulatory elements."
Natural_variation_in_DNA_methylation_homeostasis_and_the_emergence_of_epialleles
code for paper "Natural variation in DNA methylation homeostasis and the emergence of epialleles"
Heterochromatin-quantitative-epiallele-formation
Heterochromatin is a quantitative trait locus associated with spontaneous epiallele formation
Widespread-natural-variation-of-DNA-methylation-within-angiosperms
Information and scripts used in paper "Widespread natural variation of DNA methylation within angiosperms"
covid19-forecast-hub-evaluation
Evaluation of models from the COVID-19 Forecast Hub (https://github.com/reichlab/covid19-forecast-hub). These models are submitted weekly to the CDC to help inform public health decision-making.
dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
GAL
Genome Annotation Library - A perl toolkit for working with SO compliant genome annotations
Identifying-transcription-factor-DNA-interactions-using-machine-learning
Identifying transcription factor-DNA interactions using machine learning
jbscripts
cutsom scripts for JBrowse
methylpy
methylpy is a whole genome bisulfite sequencing analysis pipeline initiated by Mattew D. Schultz.
somatic-epigenetic-mutation-poplar
Analysis scripts used in "The somatic genetic and epigenetic mutation rate in wild long-lived perennial Populus trichocarpa"