Drawing cis-interactions in Ensembl

Drawing cis-interactions in Ensembl

As we announced in our e80 release post, we rolled out a prototype display for cis-regulatory interactions, essentially arches connecting any two elements on the same chromosome. This was mainly designed to display your eQTL or Hi-C with little effort, based on the WashU Continue reading Drawing cis-interactions in Ensembl

The Ensembl Regulatory Build – the Track Hub

The brand new Ensembl Regulatory Build on the new GRCh38 human assembly has been released in Ensembl 76. This involved a complete redesign of the build process with a new statistically rigorous logic, a streamlining all the backend processes and a remapping and Continue reading The Ensembl Regulatory Build – the Track Hub

Computing Ensembl’s New Regulatory Annotation

Computing Ensembl's New Regulatory Annotation

We described in a previous post Ensembl’s new regulatory annotation of the genome. Now, we will go in greater detail into how we computed it. We started by running ChromHMM over 17 cell types, using publicly available ENCODE and Roadmap Continue reading Computing Ensembl’s New Regulatory Annotation

The New Ensembl Regulatory Annotation

The New Ensembl Regulatory Annotation

GWAS after GWAS return statistically significant hits that are hard to interpret because they fall outside of coding regions, and this begs for more functional annotation of regulatory regions. We at Ensembl have been providing such an annotation for a Continue reading The New Ensembl Regulatory Annotation

WiggleTools: a pocket calculator for very large datasets

WiggleTools: a pocket calculator for very large datasets

We are pleased to announce a new bioinformatics application, WiggleTools, described in a recent Application Note in Bioinformatics. It allows you to quickly and conveniently compute statistics across many (up to the hundreds) of genome-wide datasets. WiggleTools is first a data summary tool. It collapses Continue reading WiggleTools: a pocket calculator for very large datasets

ENCODE integrative analysis data available in Ensembl

ENCODE integrative analysis data available in Ensembl

We are pleased to announce that we are now providing access to the ENCODE integrative analysis data from within Ensembl. These analyses bring together a multitude of experiments targeted at determining functional elements in the human genome sequence. This data Continue reading ENCODE integrative analysis data available in Ensembl