epigenomics

EpiRegio: analysis and retrieval of regulatory elements linked to genes

A current challenge in genomics is to interpret non-coding regions and their role in transcriptional regulation of possibly distant target genes. Genome-wide association studies show that a large part of genomic variants are found in those non-coding …

Analysing large-scale epigenomic data

Large amounts of epigenomic data are publicly available, yet their retrieval for downstream analysis is a research bottleneck. Typically, users download huge files that span the entire genome, even if they are only interested in a small subset (e.g. …

Analysing large-scale epigenomic data with DeepBlue

While large amounts of epigenomic data are publicly available, their retrieval in a form suitable for downstream analysis is a bottleneck in current research. In a typical analysis, users are required to download huge files that span the entire …

DeepBlueR

A bioconductor package for accessing the DeepBlue epigenome analysis web server.

An ontology-based method for assessing batch effect adjustmentapproaches in heterogeneous datasets

International consortia such as the Genotype-Tissue Expression(GTEx) project, The Cancer Genome Atlas (TCGA) or theInternational Human Epigenetics Consortium (IHEC) have produceda wealth of genomic datasets with the goal of advancing ourunderstanding …

DeepBlueR: large-scale epigenomic analysis in R

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets