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Box 1 Resources for mapping and analyzing allelespecific epigenetic marks

From: Genetic–epigenetic interactions in cis: a major focus in the post-GWAS era

Analytical software

Applications

URL

Reference

Bismark

Bis-seq aligner and methylation caller

http://www.bioinformatics.babraham.ac.uk/projects/bismark/

[169]

BSMAP

Bis-seq aligner

http://lilab.research.bcm.edu/dldcc-web/lilab/yxi/bsmap/bsmap-2.90.tgz

[170]

Bison

Bis-seq aligner and methylation caller

https://github.com/dpryan79/bison

[171]

Bis-SNP

Bis-seq SNP caller

http://people.csail.mit.edu/dnaase/bissnp2011/

[172]

BS-SNPer

Bis-seq SNP caller

https://github.com/hellbelly/BS-Snper

[173]

SNPsplit

Allele-specific alignment sorting

http://www.bioinformatics.babraham.ac.uk/projects/SNPsplit/

[174]

amrfinder

ASM inference from bis-seq

http://smithlabresearch.org/software/amrfinder/

[175]

R package epiG

ASM inference from bis-seq and NOMe-seq data

https://github.com/vincent-dk/epiG

[176]

R package atSNP

Allele-specific transcription factor binding affinity testing

https://github.com/chandlerzuo/atSNP

[177]

Database

Data class

URL

Reference

mQTLdb

mQTL

http://www.mqtldb.org/

[111]

Essex

mQTL

http://epigenetics.essex.ac.uk/mQTL/

[112]

SCAN

mQTL, eQTL

http://www.scandb.org/newinterface/about.html

[178]

SZDB

GWAS, mQTL, eQTL, DM, DE

http://www.szdb.org/index.html

[179]

AlleleDB

ASTF, ASE in LCLs

http://alleledb.gersteinlab.org/

[47]

GRASP

GWAS SNPs, eQTLs, mQTLs, pQTLs, mirQTL

https://grasp.nhlbi.nih.gov/Overview.aspx

[46]

GTEX

eQTLs multiple tissues

https://gtexportal.org/home/

[180]

RegulomeDB

SNP functional annotation (chromatin, TF peaks and binding affinity, DNAse, eQTLs)

http://regulomedb.org/

[20]

SNP2TFBS

SNPs affecting predicted TF binding affinity

http://ccg.vital-it.ch/snp2tfbs/

[181]

Central web sites for human epigenome projects

NIH Roadmap Epigenomics Project

http://www.roadmapepigenomics.org/

International Human Epigenome Consortium (IHEC)

http://ihec-epigenomes.org/