Epigenetic News

EpiGenie
Epigenetics & Non-Coding RNA News, Reviews, Interviews and Technology

Data portals

The Cancer Genoma Atlas (TCGA)
The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing.

Encode project (ENCyclopedia Of DNA Elements)
The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

NIH Roadmap Epigenomics Mapping Consortium
The goal of Roadmap Epigenomics Mapping Consortium is to produce a public resource of human epigenomic data to catalyze basic biology and disease-oriented research.

FANTOM (Functional ANnoTation Of the Mammalian genome)
FANTOM is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes.

BLUEPRINT
Epigenomic mapping of distinct types of haematopoietic cells from healthy individuals and on their malignant leukaemic counterparts.

Oncomine
Web application that integrates and unifies high-throughput cancer profiling data so that target expression across a large volume of cancer types, subtypes, and experiments can be assessed online.

Gene Expression Omnibus (GEO)
A public functional genomics data repository supporting MIAME-compliant data submissions.

Tools

The R Project for Statistical Computing
R is a free software environment for statistical computing and graphics.

Bioconductor
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.

GATK
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze next-generation sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.

SAMtools
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

BEDtools
Allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

Homer
Software for motif discovery and next generation sequencing analysis.

MACS
Model-based Analysis for ChIP-Seq.

Bismark
A program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.

Bowtie
An ultrafast, memory-efficient short read aligner.

Trim Galore
A wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).

Amp-errbs
This pipeline aligns RRBS and ERRBS reads to given genomes and calls for per base DNA methylation scores.

methylKit
MethylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants.

eDMR
Optimized DMR analysis based on bimodal normal distribution model and cost function for regional methylation analysis.

BSMAP
BSMAP is a short reads mapping software for bisulfite sequencing reads.

Minfi
Tools for analyzing and visualizing Illumina's 450k array data.

GREAT
Genomic Regions Enrichment of Annotations Tool (GREAT) predicts functions of cis-regulatory regions.

The Galaxy project
Galaxy is an open, web-based platform for data intensive biomedical research.

Circos
Circos is a software package for visualizing data and information.

Roadmap epigenome project protocols database
Protocols in epigenetics.

CGI Hunter
A software tool for exhaustive CpG island annotation.

MEDIPS
Software for the analysis of MeDIP-seq data.

SeqMonk
A tool to visualise and analyse high throughput mapped sequence data.

Forums

SEQanswers
The next generation sequencing community.

Seminars in Toronto

Cette Semaine
Listings of seminars from UoT and affiliated hospitals.

Genome browsers

UCSC
UCSC Genome Browser.

Human Epigenome Browser from WashU
A cutting-edge resource for visualizing and interacting with whole-genome datasetsr.

Integrative Genomics Viewer
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.