A tutorial on structural variant calling for short read sequencing data

Comprehensive design of CRISPR gRNAs for nucleases and base editors

This repository serves as a valuable resource for individuals engaged in data exploration, statistical analysis, and research within the domains of plant breeding, genetics, statistics, and genomics. The purpose of this repository is to share a collection of R codes that can be utilized by others for their own data analysis projects

Structural variant calling tutorial using long-reads.

R package for annotating and parsing transposable elements-associated data

Genetic Algorithm implementation to study haplotypes of genomic features

This repository is the current repository for our Jones et al. 2024 manuscript titled Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage.

Framework for investigation of cell-type-specific regulation and expression in rare disease

Scripts used for analysis of single cell RNA-Seq data presented in Markos 2024 paper.

Data for Smith et al. 2021 in Ecology and Evolution

This is a TxDb package created for Coffea arabica (coffee).

Sparse factorization framework to integrate GWAS studies and identify shared latent genetic components

To perform RNA-Seq data analysis and calculate length-scaled transcripts per million (TPM) values using the Salmon tool and the GenomicFeatures package in R.