PINES – Phenotype-Informed Noncoding Element Scoring

PINES

:: DESCRIPTION

PINES evaluates the functional impact of noncoding variants by integrating diverse epigenetic annotations, utilizing genomic annotations most relevant to phenotypes of interest.

::DEVELOPER

SUNYAEV LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

PINES

:: MORE INFORMATION

Citation

Bodea CA, Mitchell AA, Bloemendal A, Day-Williams AG, Runz H, Sunyaev SR.
PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants.
Genome Biol. 2018 Oct 25;19(1):173. doi: 10.1186/s13059-018-1546-6. PMID: 30359302; PMCID: PMC6203199.

LARVA – Large-scale Analysis of Variants in noncoding Annotations

LARVA

:: DESCRIPTION

LARVA is a computational framework designed to facilitate the study of noncoding variants. It addresses issues that have made it difficult to derive an accurate model of the background mutation rates of noncoding elements in cancer genomes.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LARVA

:: MORE INFORMATION

Citation:

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.
Lochovsky L, Zhang J, Fu Y, Khurana E, Gerstein M.
Nucleic Acids Res. 2015 Sep 30;43(17):8123-34. doi: 10.1093/nar/gkv803.