Machine Learning in Omics: Integration of Metagenomics and Metabolomics.

A GLUE project for hepatitis B virus (HBV).

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

vcfdist: Accurately benchmarking phased variant calls

Analysis of SNP variants, derived from chip array genotyping and HTS sequencing

Comprehensive design of CRISPR gRNAs for nucleases and base editors

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.

Genomics Carpentries Workshop at Rutgers University, April 25-26, 2024

This repository houses the Genomic Sequence Comparison Code (GSCC), a collection of Python scripts designed for genomic sequence analysis. Whether you're comparing suspected sequences with known reference sequences or delving into bioinformatics, GSCC provides versatile tools for pairwise alignment. Feel free to explore!

Bioinformatics on GCP, AWS or Azure

Tool to estimate deltas for sequence sets and answer questions about relative contribution

R package for annotating and parsing transposable elements-associated data

Supervised classification of various species DNA sequences using FFT and Machine Learning.

Extraction of genomic background set of DNA sequences for a given foreground set of sequences for subsequent de novo motif discovery

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

Automating WES Data analysis (primarily of Cancer).

Using NVIDIA Deepmind's Nucleotide Transformer to generate embeddings for yeast genomes.

Genetic Algorithm implementation to study haplotypes of genomic features

NLR-Assembler is a command line tool for improving RenSeq Assemblies using linked-read sequencing by 10x Genomics.

A web application for interactive visualization and exploratory data analysis of variant call matrices