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
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