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 | [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 | [173] | |
SNPsplit | Allele-specific alignment sorting | [174] | |
amrfinder | ASM inference from bis-seq | [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 | [111] | |
Essex | mQTL | [112] | |
SCAN | mQTL, eQTL | [178] | |
SZDB | GWAS, mQTL, eQTL, DM, DE | [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 | [180] | |
RegulomeDB | SNP functional annotation (chromatin, TF peaks and binding affinity, DNAse, eQTLs) | [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 | |||
International Human Epigenome Consortium (IHEC) |