| Identification of LD proxies |
LDlink |
https://ldlink.nci.nih.gov/ |
| Statistical fine-mapping |
BIMBAM |
http://stephenslab.uchicago.edu/software.html |
| MANTRA |
Morris51
|
| CAVIARBF |
https://bitbucket.org/Wenan/caviarbf |
| CAVIAR |
http://genetics.cs.ucla.edu/caviar/ |
| PAINTOR |
https://github.com/gkichaev/PAINTOR_V3.0 |
| fGWAS |
https://github.com/joepickrell/fgwas |
| PICS |
https://pubs.broadinstitute.org/pubs/finemapping/pics.php |
| funciSNP |
https://doi.org/doi:10.18129/B9.bioc.FunciSNP |
| FINEMAP |
http://www.christianbenner.com/ |
| GenoWAP |
http://genocanyon.med.yale.edu/GenoWAP |
| DAP |
https://github.com/xqwen/dap |
| Annotation of splice variants |
HEXplorer |
http://www2.hhu.de/rna/html/hexplorer_score.php |
| ASSA |
http://splice.uwo.ca/ |
| MaxEntScan |
http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html |
| GeneSplicer |
http://ccb.jhu.edu/software/genesplicer/ |
| Human Splicing Finder |
http://www.umd.be/HSF3/ |
| Annotation of coding variants |
PolyPhen2 |
http://genetics.bwh.harvard.edu/pph2/ |
| SIFT |
http://provean.jcvi.org/index.php |
| CONDEL |
http://bbglab.irbbarcelona.org/fannsdb/ |
| MAPPIN |
https://doi.org/10.6084/m9.figshare.4639789 |
| dbNSFP |
https://sites.google.com/site/jpopgen/dbNSFP |
| MutationTaster2 |
http://www.mutationtaster.org/ |
| Annotation of noncoding and coding variants |
CADD |
https://cadd.gs.washington.edu/ |
| PredictSNP2 |
https://loschmidt.chemi.muni.cz/predictsnp2/ |
| FATHMM-MKL |
http://fathmm.biocompute.org.uk/ |
| EIGEN |
http://www.columbia.edu/∼ii2135/eigen.html |
| Annotation of noncoding variants |
GWAVA |
https://www.sanger.ac.uk/sanger/StatGen_Gwava |
| ARVIN |
https://github.com/gaolong/arvin |
| SNVrap |
http://jjwanglab.org/snvrap |
| DANN |
https://cbcl.ics.uci.edu/public_data/DANN/ |
| DanQ |
https://github.com/uci-cbcl/DanQ |
| SNPDelScore |
https://www.ncbi.nlm.nih.gov/research/snpdelscore |
| deltaSVM |
http://www.beerlab.org/deltasvm/ |
| DeepSEA |
http://deepsea.princeton.edu/job/analysis/create/ |
| 3DSNP |
http://cbportal.org/3dsnp/ |
| HaploReg |
http://pubs.broadinstitute.org/mammals/haploreg/haploreg.php |
| SNiPA |
http://snipa.helmholtz-muenchen.de/snipa3/ |
| GREGOR |
https://genome.sph.umich.edu/wiki/GREGOR |
| GARFIELD |
https://www.ebi.ac.uk/birney-srv/GARFIELD/ |
| RegulomeDB |
http://www.regulomedb.org/ |
| Regulatory datasets |
ENCODE |
https://www.encodeproject.org/ |
| Roadmap Epigenomics |
http://www.roadmapepigenomics.org/ |
| Fantom5 |
http://fantom.gsc.riken.jp/5/ |
| VISTA enhancer |
https://enhancer.lbl.gov/ |
| cistromeDB |
http://cistrome.org/db/#/ |
| Blueprint |
http://www.blueprint-epigenome.eu/ |
| Databases of transcription factor binding motifs |
JASPAR |
http://jaspar.genereg.net/ |
| HOCOMOCO |
http://hocomoco11.autosome.ru/ |
| PWMtools |
https://ccg.vital-it.ch/pwmtools/ |
