Lab Resources

Tools, data, and code from the Monroe Lab

Code & Software

ResourceDescriptionLink
Monroe Lab GitHubCode and analysis pipelines from lab publicationsGitHub
polymorphology2A general R toolkit for handling genomic data. Focuses on analyzing polymorphisms in the context of genome features such as gene bodies, epigenome features, and SBS mutation profiles.GitHub
kolibriKernel-Operations for Long-read Insertion, Breakpoint & Recombination Inspection. An R-based toolkit for inspecting long-read alignments (PacBio/ONT) to find, group, and visualize split reads indicating assembly errors, structural variation, transposition, recombination, or other complex genome events.GitHub
reCYCLingRepeat Element Cyclical Evolutionary Simulations in Genomes. An R toolkit for simulating the evolution of tandem repeat arrays and analyzing the resulting arrays using diagnostics that mirror how we interrogate real repeat architectures (e.g., arrays identified with TRASH-like workflows).GitHub
ggenomicsAn R package for visualizing genomic features using ggplot2. Developed in the Monroe Lab for flexible, publication-quality plots of genome-wide data.GitHub
ggideoAn R package for creating genomic feature visualizations using ggplot2. Developed by Matt Davis for intuitive visualization of genomic intervals and features.GitHub
intronologyAn R package for intron architecture analysis, developed by Alice Pierce in the context of intron-mediated enhancement and gene body mutation rate research.GitHub

Funding Opportunities

Resources for prospective lab members:

ResourceDescriptionLink
Graduate Funding OpportunitiesCompiled list of funding for graduate studentsDownload
Postdoc Funding OpportunitiesCompiled list of funding for postdoctoral researchersDownload

Pistachio Genomics

ResourceDescriptionLink
PistachiomicsGenomic, proteomic, and transcriptomic resources for the genus Pistacia, produced by the Monroe Lab and supported by the California Pistachio Research Boardpistachiomics.sf.ucdavis.edu

Data Depositions

Cassava Whole Genome Resequencing

Whole-genome resequencing (~20x coverage) for approximately 400 cassava landraces, generated for our cassava population genomics study.

DatasetLink
NCBI BioProject PRJNA1228154View on NCBI

Cassava Pan-genome VCF

A large-scale VCF compiled from all whole-genome sequencing data available to date in cassava — over 1,000 genotypes. Published alongside our cassava landrace paper in New Phytologist. Ready-to-use variant calls for population genetic, GWAS, and diversity analyses in cassava.

DatasetLink
Zhao et al. 2026 — CassavaBase data repositorycassavabase.org

Walnut Genome Assembly and Somatic Mutation in Tissue Culture

Data associated with Davis et al. 2025 — Extreme somatic mutation variation through time and space in walnut clones · bioRxiv. Includes raw sequencing data, the primary genome assembly and annotation of Juglans regia cv. ‘Chandler’, and both haplotype-resolved assemblies.

DatasetLink
Raw sequencing data — NCBI BioProject PRJNA1271128View on NCBI
Primary genome assembly (J. regia ‘Chandler’) — NCBI BioProject PRJNA1289367View on NCBI
Haplotype A (hap1) assembly — NCBI BioProject PRJNA1289368View on NCBI
Haplotype B (hap2) assembly — NCBI BioProject PRJNA1289370View on NCBI

Pistachio “In a Nutshell” Genome Project

Data associated with our pistachio reference genome paper in New Phytologist. These data were used to generate and annotate the Kerman reference genome and include:

  • PacBio HiFi long-read data
  • Omni-C data
  • Iso-Seq RNA sequencing data
  • Short-read RNA sequencing data for genome annotation
DatasetLink
NCBI BioProject PRJNA1114109View on NCBI
NCBI BioProject PRJNA1049825View on NCBI

Arabidopsis MSH6 Study

Ultra high-depth (~300x) short-read sequencing of wild-type and msh6 knockout Arabidopsis thaliana lines, used to analyze germline and somatic mutation effects of MSH6 deficiency.

Associated publication: Quiroz et al. — H3K4me1 recruits DNA repair proteins in plants · The Plant Cell

DatasetLink
NCBI BioProject PRJNA1039302View on NCBI