Software from our Lab

Here we present an accessible, interactive GenePattern notebook for the analysis of copy number variation using Illumina Infinium DNA methylation arrays. The notebook provides a graphical user interface to a workflow using the R/Bioconductor packages minfi and conumee. The environment allows analysis to be performed without the installation of the R software environment, the packages and dependencies, and without the need to write or manipulate code.

GenePattern Module: MethylationCNVAnalysis

The package is focused on the detection of correlation between expressed genes and selected epigenomic signals i.e. enhancers obtained from ChIP-seq data within topologically associated domains (TADs). Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.

Bioconductor page: InTAD

qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.

Bioconductor page: QSEA

MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). MEDIPS provides functionalities for the analysis of various quantitative sequencing data types (e.g., ChIP-seq, MBD-seq, CMS-seq, and others), including calculation of differential coverage between sample groups and saturation and correlation analysis.

Bioconductor page: MEDIPS

This GitHub page contains the repositories for the tools and analysis developed as part of the genetic analysis projects undertaken by our lab.