Software from our Lab

ecDNA Childhood Cancer Catalog

We present an accessible, interactive web-based portal for exploring the ecDNA Childhood Cancer Catalog. This resource provides streamlined access to sample-level data, annotations, and visualizations from the ecDNA PedPanCancer study, enabling users to efficiently retrieve and interpret study findings.

Childhood Cancer Data Initiative: ecDNA Childhood Cancer Catalog

GenePattern Notebook – CNV analysis of Illumina methylation arrays

This interactive GenePattern notebook analyzes copy number variation using Illumina Infinium DNA methylation arrays. It provides a GUI-based workflow using R/Bioconductor packages like minfi and conumee, without requiring R installation or coding.

GenePattern Module: MethylationCNVAnalysis

InTAD detects correlations between gene expression and enhancer activity (e.g., from ChIP-seq data) within topologically associated domains (TADs). It offers flexible parameters and built-in visualization tools.

Bioconductor page: InTAD

QSEA analyzes MeDIP-seq and similar enrichment-based sequencing data, supporting other assays like ChIP-seq and MBD-seq. It enables differential enrichment analysis between groups.

Bioconductor page: QSEA

MEDIPS provides analysis tools for MeDIP-seq data, including differential coverage analysis, correlation, and quality metrics. It supports additional data types like ChIP-seq and CMS-seq.

Bioconductor page: MEDIPS

Explore Chavez Lab's GitHub repository, which hosts open-source tools, workflows, and analyses developed for various genomic research projects.

GitHub page: Chavez Lab