CpGPT: a Foundation Model for DNA Methylation.

Information Theoretic Framework for Paired Single Cell Gene Expression and TCR Sequencing

Vector representations of gene co-expression in single cell RNAseq.

🔧 .files, including ~/.macos — sensible hacker defaults for macOS

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes

R package for misc tools

R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.

R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework

Tutorials and training material for the H2O Machine Learning Platform

Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.

LowRankModels.jl is a julia package for modeling and fitting generalized low rank models.

R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework

Config files used to define parameters specific to compute environments at different Institutions

❗ This is a read-only mirror of the CRAN R package repository. rBMF — Boolean Matrix Factorization

Scalable GenomicRanges based class for storing, manipulating, and querying genomic matrices and pairwise features.

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

Updated implementation of the GSEA-P R application for modern R distributions

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.